Filtering with a piece of cotton / cig filter won't get rid of particles smaller than 50 micron (the width of a piece of hair), but it's still much better than not filtering at all.
Filtering it won't reduce the potency at all. Most base dissolves easily in water without too many particles left. If your gear won't dissolve readily in water and gets stuck in the filter, you shoudn't be injecting it anyway.
Even if it appears to dissolve into a clear-looking solution, there can still be particles present than can cause damage to the veins, heart and lungs. Filtering with cotton isn't ideal, but it will at least remove some of the crap from the mix.