I recently did a scan with Malwarebytes and it came up saying

Files Infected:
c:\WINDOWS\ap (Trojan.Agent) -> No action taken.

Now I scanned with Spybot, SUPER Anti Spyware, AVG, Trend Housecall, Kaspersky online, Freefixer and hijackthis and none of them found anything. Should I delete the file or is it a normal file? Any help is appreciated.

Thanks,
Carl H.

Remove it. Malwarebytes backs up all it removes. If it would happen to be a false positive then you could restore it. But, since there is no "ap" file I would say it is not a false positive.
Malwarebytes is the top of the line right now, beats all others hands down.
Was this a quick scan or full scan? If you suspect something a full scan should always be done OR if something is found with a quick scan then a full scan should also be done. Quick scan doesn't scan all files, full scan does.
When using Malwarebytes these are the instructions you should follow:
# Be sure a checkmark is placed next to Update Malwarebytes' Anti-Malware and Launch Malwarebytes' Anti-Malware, then click Finish.
# If an update is found, it will download and install the latest version.
# Once the program has loaded, select Perform full scan, then click Scan.
# When the scan is complete, click OK, then Show Results to view the results.
# Be sure that everything is checked, and click Remove Selected.
# When MBA-M finishes, Notepad will open with the log. Please save it where you can find it easily. The log can also be opened by going to Start > All Programs > Malwarebytes' Anti-Malware > Logs > log-date.txt.
Then the computer should be rebooted. Many items cannot be fully removed until the computer is rebooted so this should always be done as a matter of course when something is found by MBA-M.

AVG, Trend Housecall, Kaspersky online, are virus scanners and will not necessarily find a trojan, which is not a virus. HiJackThis is not considered a search tool especially, it is generally the last tool you run AFTER all cleaning has been done. It also is not to be considered a removal tool.
We truly have no idea what you have found since you posted no logs. So other than general advice we cannot tell you what else to do, except allow it to remove the item found. We need to see those full logs.

It was a full scan, I never quick scan unless I right click on a specific file and scan it. I also always check for updates with all my scanning software. Here's the log from Malwarebytes that I just scanned

Malwarebytes' Anti-Malware 1.39
Database version: 2483
Windows 5.1.2600 Service Pack 3

7/22/2009 10:36:22 PM
mbam-log-2009-07-22 (22-36-22).txt

Scan type: Full Scan (C:\|)
Objects scanned: 206889
Time elapsed: 45 minute(s), 54 second(s)

Memory Processes Infected: 0
Memory Modules Infected: 0
Registry Keys Infected: 0
Registry Values Infected: 0
Registry Data Items Infected: 0
Folders Infected: 0
Files Infected: 1

Memory Processes Infected:
(No malicious items detected)

Memory Modules Infected:
(No malicious items detected)

Registry Keys Infected:
(No malicious items detected)

Registry Values Infected:
(No malicious items detected)

Registry Data Items Infected:
(No malicious items detected)

Folders Infected:
(No malicious items detected)

Files Infected:
c:\WINDOWS\ap (Trojan.Agent) -> Quarantined and deleted successfully.

Did you reboot the computer?
Now do the following:
Download HiJackThis. Run a full system scan and save the log.
Post back here with that log.

commented: Quick and knowledgeable +3

Yes I rebooted and I just ran a hijack this and checked it on an analyizer at http://www.hijackthis.de/en#anl and it didn't find anythng sketchy... Here's the log

Logfile of Trend Micro HijackThis v2.0.2
Scan saved at 11:00:56 PM, on 7/22/2009
Platform: Windows XP SP3 (WinNT 5.01.2600)
MSIE: Internet Explorer v7.00 (7.00.6000.16850)
Boot mode: Normal

Running processes:
C:\WINDOWS\System32\smss.exe
C:\WINDOWS\system32\winlogon.exe
C:\WINDOWS\system32\services.exe
C:\WINDOWS\system32\lsass.exe
C:\WINDOWS\system32\nvsvc32.exe
C:\WINDOWS\system32\svchost.exe
C:\WINDOWS\system32\svchost.exe
C:\WINDOWS\system32\svchost.exe
C:\WINDOWS\system32\LEXBCES.EXE
C:\WINDOWS\system32\spoolsv.exe
C:\WINDOWS\system32\LEXPPS.EXE
C:\WINDOWS\Explorer.EXE
C:\PROGRA~1\AVG\AVG8\avgtray.exe
C:\PROGRA~1\AVG\AVG8\avgwdsvc.exe
C:\WINDOWS\system32\ctfmon.exe
C:\Program Files\Diskeeper Corporation\Diskeeper\DkService.exe
C:\Program Files\Logitech\SetPoint\SetPoint.exe
C:\PROGRA~1\AVG\AVG8\avgrsx.exe
C:\PROGRA~1\AVG\AVG8\avgnsx.exe
C:\WINDOWS\system32\PnkBstrA.exe
C:\WINDOWS\system32\PnkBstrB.exe
C:\WINDOWS\system32\svchost.exe
C:\Program Files\Viewpoint\Common\ViewpointService.exe
C:\PROGRA~1\AVG\AVG8\avgemc.exe
C:\Program Files\Common Files\Logishrd\KHAL2\KHALMNPR.EXE
C:\Program Files\AVG\AVG8\avgcsrvx.exe
C:\Program Files\Teamspeak2_RC2\TeamSpeak.exe
C:\Program Files\Malwarebytes' Anti-Malware\mbam.exe
C:\Program Files\Internet Explorer\iexplore.exe
C:\Program Files\Trend Micro\HijackThis\HijackThis.exe

R1 - HKCU\Software\Microsoft\Internet Explorer\Main,Search Page = http://go.microsoft.com/fwlink/?LinkId=54896
R0 - HKCU\Software\Microsoft\Internet Explorer\Main,Start Page = about:blank
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Default_Page_URL = http://go.microsoft.com/fwlink/?LinkId=69157
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Default_Search_URL = http://go.microsoft.com/fwlink/?LinkId=54896
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Search Page = http://go.microsoft.com/fwlink/?LinkId=54896
R0 - HKLM\Software\Microsoft\Internet Explorer\Main,Start Page = http://go.microsoft.com/fwlink/?LinkId=69157
R0 - HKLM\Software\Microsoft\Internet Explorer\Search,SearchAssistant =
R0 - HKLM\Software\Microsoft\Internet Explorer\Search,CustomizeSearch =
R1 - HKCU\Software\Microsoft\Windows\CurrentVersion\Internet Settings,ProxyOverride = local
O2 - BHO: AcroIEHelperStub - {18DF081C-E8AD-4283-A596-FA578C2EBDC3} - C:\Program Files\Common Files\Adobe\Acrobat\ActiveX\AcroIEHelperShim.dll
O2 - BHO: WormRadar.com IESiteBlocker.NavFilter - {3CA2F312-6F6E-4B53-A66E-4E65E497C8C0} - C:\Program Files\AVG\AVG8\avgssie.dll
O2 - BHO: Spybot-S&D IE Protection - {53707962-6F74-2D53-2644-206D7942484F} - C:\Program Files\Spybot - Search & Destroy\SDHelper.dll
O2 - BHO: ibj-clan Toolbar - {659125cc-3420-4139-98ea-5d61dc31f913} - C:\Program Files\ibj-clan\tbibj1.dll
O2 - BHO: Windows Live ID Sign-in Helper - {9030D464-4C02-4ABF-8ECC-5164760863C6} - C:\Program Files\Common Files\Microsoft Shared\Windows Live\WindowsLiveLogin.dll
O2 - BHO: Adobe PDF Conversion Toolbar Helper - {AE7CD045-E861-484f-8273-0445EE161910} - C:\Program Files\Common Files\Adobe\Acrobat\ActiveX\AcroIEFavClient.dll
O2 - BHO: Java(tm) Plug-In 2 SSV Helper - {DBC80044-A445-435b-BC74-9C25C1C588A9} - C:\Program Files\Java\jre6\bin\jp2ssv.dll
O2 - BHO: JQSIEStartDetectorImpl - {E7E6F031-17CE-4C07-BC86-EABFE594F69C} - C:\Program Files\Java\jre6\lib\deploy\jqs\ie\jqs_plugin.dll
O2 - BHO: WinAVI FLVSense - {E8DF67A1-B618-4F3F-9E7C-CBE175ADEF5B} - C:\Program Files\WinAVI FLV Converter\FLVTune.dll
O2 - BHO: SmartSelect - {F4971EE7-DAA0-4053-9964-665D8EE6A077} - C:\Program Files\Common Files\Adobe\Acrobat\ActiveX\AcroIEFavClient.dll
O3 - Toolbar: ibj-clan Toolbar - {659125cc-3420-4139-98ea-5d61dc31f913} - C:\Program Files\ibj-clan\tbibj1.dll
O3 - Toolbar: Adobe PDF - {47833539-D0C5-4125-9FA8-0819E2EAAC93} - C:\Program Files\Common Files\Adobe\Acrobat\ActiveX\AcroIEFavClient.dll
O4 - HKLM\..\Run: [AVG8_TRAY] C:\PROGRA~1\AVG\AVG8\avgtray.exe
O4 - HKLM\..\Run: [NvCplDaemon] RUNDLL32.EXE C:\WINDOWS\system32\NvCpl.dll,NvStartup
O4 - HKLM\..\Run: [Kernel and Hardware Abstraction Layer] KHALMNPR.EXE
O4 - HKCU\..\Run: [ctfmon.exe] C:\WINDOWS\system32\ctfmon.exe
O4 - Global Startup: Logitech SetPoint.lnk = C:\Program Files\Logitech\SetPoint\SetPoint.exe
O8 - Extra context menu item: &Download FLV by WinAVI... - C:\Program Files\WinAVI FLV Converter\flv_link.htm
O9 - Extra button: Create Mobile Favorite - {2EAF5BB1-070F-11D3-9307-00C04FAE2D4F} - C:\PROGRA~1\Microsoft ActiveSync\INetRepl.dll
O9 - Extra button: (no name) - {2EAF5BB2-070F-11D3-9307-00C04FAE2D4F} - C:\PROGRA~1\Microsoft ActiveSync\INetRepl.dll
O9 - Extra 'Tools' menuitem: Create Mobile Favorite... - {2EAF5BB2-070F-11D3-9307-00C04FAE2D4F} - C:\PROGRA~1\Microsoft ActiveSync\INetRepl.dll
O9 - Extra button: Research - {92780B25-18CC-41C8-B9BE-3C9C571A8263} - C:\PROGRA~1\MICROS~2\Office12\REFIEBAR.DLL
O9 - Extra button: WinAVI FLV Manager - {DE365254-2F9B-4908-9E3A-7AAA6EC90BCC} - C:\Program Files\WinAVI FLV Converter\FLVTune.dll
O9 - Extra 'Tools' menuitem: WinAVI FLV Manager - {DE365254-2F9B-4908-9E3A-7AAA6EC90BCC} - C:\Program Files\WinAVI FLV Converter\FLVTune.dll
O9 - Extra button: (no name) - {DFB852A3-47F8-48C4-A200-58CAB36FD2A2} - C:\Program Files\Spybot - Search & Destroy\SDHelper.dll
O9 - Extra 'Tools' menuitem: Spybot - Search && Destroy Configuration - {DFB852A3-47F8-48C4-A200-58CAB36FD2A2} - C:\Program Files\Spybot - Search & Destroy\SDHelper.dll
O9 - Extra button: (no name) - {e2e2dd38-d088-4134-82b7-f2ba38496583} - C:\WINDOWS\Network Diagnostic\xpnetdiag.exe
O9 - Extra 'Tools' menuitem: @xpsp3res.dll,-20001 - {e2e2dd38-d088-4134-82b7-f2ba38496583} - C:\WINDOWS\Network Diagnostic\xpnetdiag.exe
O9 - Extra button: Messenger - {FB5F1910-F110-11d2-BB9E-00C04F795683} - C:\Program Files\Messenger\msmsgs.exe
O9 - Extra 'Tools' menuitem: Windows Messenger - {FB5F1910-F110-11d2-BB9E-00C04F795683} - C:\Program Files\Messenger\msmsgs.exe
O9 - Extra button: ZDelete Auto-Cleaner - {EB7F329E-F14E-48ae-AB69-4E28C492D382} - C:\Program Files\LSoft Technologies\Active ZDelete\ZDelete.exe (HKCU)
O16 - DPF: {6414512B-B978-451D-A0D8-FCFDF33E833C} (WUWebControl Class) - http://update.microsoft.com/windowsupdate/v6/V5Controls/en/x86/client/wuweb_site.cab?1246485703843
O18 - Protocol: linkscanner - {F274614C-63F8-47D5-A4D1-FBDDE494F8D1} - C:\Program Files\AVG\AVG8\avgpp.dll
O20 - Winlogon Notify: !SASWinLogon - C:\Program Files\SUPERAntiSpyware\SASWINLO.dll
O20 - Winlogon Notify: avgrsstarter - C:\WINDOWS\SYSTEM32\avgrsstx.dll
O23 - Service: AVG Free8 E-mail Scanner (avg8emc) - AVG Technologies CZ, s.r.o. - C:\PROGRA~1\AVG\AVG8\avgemc.exe
O23 - Service: AVG Free8 WatchDog (avg8wd) - AVG Technologies CZ, s.r.o. - C:\PROGRA~1\AVG\AVG8\avgwdsvc.exe
O23 - Service: Diskeeper - Diskeeper Corporation - C:\Program Files\Diskeeper Corporation\Diskeeper\DkService.exe
O23 - Service: FLEXnet Licensing Service - Acresso Software Inc. - C:\Program Files\Common Files\Macrovision Shared\FLEXnet Publisher\FNPLicensingService.exe
O23 - Service: Google Update Service (gupdate1ca0298f5a958e2) (gupdate1ca0298f5a958e2) - Google Inc. - C:\Program Files\Google\Update\GoogleUpdate.exe
O23 - Service: InstallDriver Table Manager (IDriverT) - Macrovision Corporation - C:\Program Files\Common Files\InstallShield\Driver\1050\Intel 32\IDriverT.exe
O23 - Service: iReboot Background Service (iReboot) - Unknown owner - C:\Program Files\NeoSmart Technologies\iReboot\iRebootd.exe
O23 - Service: Java Quick Starter (JavaQuickStarterService) - Sun Microsystems, Inc. - C:\Program Files\Java\jre6\bin\jqs.exe
O23 - Service: Logitech Bluetooth Service (LBTServ) - Logitech, Inc. - C:\Program Files\Common Files\Logishrd\Bluetooth\LBTServ.exe
O23 - Service: LexBce Server (LexBceS) - Lexmark International, Inc. - C:\WINDOWS\system32\LEXBCES.EXE
O23 - Service: NMIndexingService - Nero AG - C:\Program Files\Common Files\Nero\Lib\NMIndexingService.exe
O23 - Service: NVIDIA Display Driver Service (nvsvc) - NVIDIA Corporation - C:\WINDOWS\system32\nvsvc32.exe
O23 - Service: PnkBstrA - Unknown owner - C:\WINDOWS\system32\PnkBstrA.exe
O23 - Service: PnkBstrB - Unknown owner - C:\WINDOWS\system32\PnkBstrB.exe
O23 - Service: Viewpoint Manager Service - Viewpoint Corporation - C:\Program Files\Viewpoint\Common\ViewpointService.exe

--
End of file - 8377 bytes

Thanks for your help

Unless you have purchased MBA-M there is no reason for it to be running in the background. Be sure to end that program. Viewpoint Manager Service is considered foistware. You should go to Add/Remove and uninstall Viewpoint listings. Other than those, all looks good to me.
MBA-M is recommended to be run at least weekly, Quick Scan is sufficient. If something is found then Full Scan should be done.

It was running in the background because I didn't close it out... I uninstalled viewpoint. I don't even know how it got there because I didn't download it... I usually do a spyware scan everyday or every other day while I'm out. Thanks again for your help.

Viewpoint comes in with some other program. It isn't generally called spyware but is considered foistware as I noted above since it is installed without the user's knowledge.
Are your problems solved?

Yes they are, thank you for your help. I'm sorry it took so long to answer back. Thank you again.

Carl H.

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