Plane cutting

Hi there, 

We tried to create a spiral stair so we set random points, moved them and rotated and then finally made an octree. But now we want to cut little rounds out of the planes from the boxes (but only the sides not the upper and bottom of the boxes. Has anyone any idea how to do this? we tried Brep but it only selects one side of the box and we need the four side planes of the box and we have no idea how to make holes in a plane :/ 

help?!