Cannot securely overwrite certain files.

When I try to securely overwrite certain files I get a message which says, "Not overwritten. File is resident in the MFT". What does this mean? Is there any way around this, or are these files stuck there for good?

It means that the file is small, probably under 700-800 bytes or so, and the file data is entirely resident in the Master File Table. There is no legitimate way to overwrite this data in NTFS. You could use Wipe MFT in CCleaner, part of the Wipe Free Space routine, or you could wait for them to be overwritten in the normal course of events, as many of them will be, or you could just live with it.

Allot of stuff that Recuva will outright refuse to overwrite can actually be dealt with using CCleaner's 'Wipe Free Space'!