CCleaner does not completely clean the hardrive

i just ran it it took a few hours but once it got done i ran a program to make sure all the files where over ridden. it looks like it only did about half the harddrive then i saw files that i could retrive which i did not want them on there. any suggestions of why it did not do the whole drive. i did check the mft free space

thank you

You'll have to give more info such as operating system, and which settings you used.

Did you actually try and open one of the files you said you could retrieve?

Are you using wipe space? Is the drive an active windows installation?