Stewart,
If you know where your frequencies lie in your signal, then you could write an algorithm to take them out.
Once a signal has been digitized, the signals will be aliased and frequencies will appear. Anti-aliasing is best done in the hardware. National Instruments does this through
SCXI and
SCC. You may want to look into SCC and see if you can add this to the outside of your system.
Randy Hoskin
Applications Engineer
National Instruments
http://www.ni.com/ask