There are programs that will search using the MFT on Windows NTFS volumes, e.g. open source projects:
http://sourceforge.net/projects/swiftsearch/
http://sourceforge.net/projects/ntfs-search/
They're VERY fast but the problem is that once you start going straight to the MFT you by-pass functionality such as security ACLs and shell extensions. Therefore most of these programs need to run with elevated permissions and don't necessarily produce the same results as an API based search.