Filtering PCM data in java
Audio EQ in by FFT?!? Please don't do that. CPU usage will be the least of your worries. http://blog.bjornroche.com/2012/08/why-eq-is-done-in-time-domain.html There was also a related discussion recently on the linkedin dsp group.

This post covers how to do a bell filter in the time domain, but it's extremely similar to create a low pass (actually a low pass is easier), and will be MUCH easier than trying to do an FFT (which won't do what you want anyway): http://blog.bjornroche.com/2012/08/basic-audio-eqs.html

You won't have to worry at all about memory (it only needs 2 memory slots) and CPU usage is very low. Plus latency is minimal. The final implementation is like 10 lines of code.

The original "cookbook" reference is here: http://www.musicdsp.org/files/Audio-EQ-Cookbook.txt

Now, that said, this filter may not do for your purpose, but you haven't really made it clear what that is, so please feel free to clarify.