On cleaning and then defragmenting NTFS a warning message appears: The MFT usage was currently 99 percent of the total MFT size, which indicates it is likely the MFT will become fragmented. What do...

In short, the message means that the MFT (Master File Table – which is like the table of contents for the hard drive) is almost full and needs to be continued in another section of the hard drive. Typically a certain amount of space is reserved at the beginning of the hard drive for the MFT. Once the MFT gets full (because of too many files) it will automatically get increased in size and continue on another part of the hard drive. (Kind of like having a Table of Contents in a book but there are more lines in it than the number of allotted pages for it. It just has to continue with the additional or new items some place else.) It is of no concern really as the system will continue to function normally. Here are some articles from Microsoft's web site that explain it in more detail.