Disk Cleanup has a lot of options when its opened from the command prompt
Click start --> Run and type in cmd type in chkdsk.exe plus one of the following switches. In the command prompt you will type in something like chkdsk.exe /X to run the desired operation.
/C Will skip the checking of cycles within the folder structure to do a much faster run of chkdsk
/I performs a not so thorough check of index entries, also making a faster run of chkdsk
/L[:size:] allows you to designate the size of the log file.
/X dismounts the drive before scanning. This is the most thorough scan available.