Squaring a block of material can be confusing at first to end up with a square block. The steps to square a block of material assume that the rear vise jaw has been indicated in both the X and Z planes as outlined in Indicating a Vise.
Machine the first flat face by placing the material in the vise and machining it flat.
Place the flat face against the rear jaw and machine the top face flat. Now we have two surfaces that are perpendicular to each other.
Rotate the material around the Y axis 180 degrees and place one parallel against the rear jaw and put the side from Step 2 against the parallel. Machine the third face and now we have 3 sides and 2 edges.
Rotate the material around the X axis 90 degrees to put the unfinished side up. Machine this side flat and now we have 4 sides and 4 edges perpendicular and square to each other.
If your starting with reasonably flat material on 4 sides you might start here. Rotate the material around the Y axis 90 degrees and using one parallel against the fixed rear jaw of the vise. Machine this face flat then with a marker put an X on it and a line on the right side. This face is perpendicular to the other faces only on the edge.
Using one parallel against the rear fixed jaw of the vise rotate the material 90 degrees in the Z axis and 180 degrees in the Y plane. This places the line you made on top of the parallel. Machine this face flat and you now have 5 faces done.
Rotate the material 180 degrees in the Y axis and you can use 2 parallels now and machine the last face flat. You now have a cube with all faces square to each other.