Hey Thomas,
the filters Karsten mentioned sound interesting. I've never really looked into those though (I guess I try to avoid Cygwin programs too much, haha). Alternatively, you could write your own IFM Data Importer. We do this quite a bit and it works fine. You need to write and compile the C/C++ code though.
On the long run, it would certainly be nice if FeFlow had features like that incorporated into the User Interface.
Cheers, Chris.