What you do is:
1) move the cylinder so that it overlaps/ intersects the cube
2) select one object (the cube), then hold shift and select the other one (the cylinder)
3) In the toolbar at the top go to Polygons/ Booleans/ Difference
And that should do it
Try experimenting with the Union and Intersection settings and which item you select first; you'll get a lot of results to play with!