move the ruler to where the 4x4 square is in the top right corner of the ruler (if the numbers are facing the "right" way on the ruler). Put the bottom edge of your square on the 4" line down from the top of the ruler and the left side of your square on the 4" line from the right edge of the ruler. Assuming that your seam lines are straight, use another measurement line on the ruler to line up with a seam line to square up the block evenly. After you are satisfied that the edges of your block are squared (even) with the 4" lines on the ruler, then cut the right edge of your square using the rotary cutter and then the top edge of your square. Turn the square so that the freshly cut edges are even with the 4" lines on the ruler and square up the other two edges.
Hope this helps and isn't too confusing!!