Digital Anti Aliasing Filter For Waveform Band Limiting
I am generating my waves in a "Raw" mathematical way, meaning that i am creating a ramp for a saw wave and my square wave consists of pure 1's and 0's. The issue is that this technique is inherently not band limited. I would like to implement low pass filter into the algorithm in order to filter of the harmonic being generated that are higher than the nyquist limit. 


You can't do this.  You've already aliased the frequencies when you generated the waves in that way.  You can't remove them with a filter.

You're essentially sampling the pure mathematical signal without using an antialiasing filter first.  It's not possible to add the antialiasing filter after sampling.  You will just filter the already-aliased signal.  Bandlimiting has to occur before sampling.  You need to change the way you generate the waveforms if you want them to be bandlimited.  You could generate them using additive synthesis, as I've demonstrated here, or you could generate them the simple way at a much higher sampling rate to minimize the aliasing, then antialias filter, then decimate.  Or you could use BLIT or BLEP, etc.  (I think those are both "reduced-aliasing" not 100% eliminated, but I'm not sure.)