Is compressing the drive space same with compressing old files?

I am looking for some clarifications regarding the compression of old files which is a selection in the disk clean up of Windows XP and Windows 2000. If I am doing the compression regularly, will that create any problem with the system files in the future? Is the ‘compress drive to save space’ option in the disk properties and the above specified compression the same or not? If this option is used for compression, will it make any problem in the future? Please help me to get out this problem. Thanks in advance.
