The math for half square triangles is to add 7/8" to the finished size. So if you want a 3" finished half-square triangle, you would cut your square 3-7/8".
I usually add 1" (cutting the square 4" in the above example), stitch, press and then sliver trim both units to a perfect 3-1/2" unfinished half-square triangle. The 3-1/2" unfinished size will measure 3" once sewn into the quilt.