Here's a short screencast showing how to create a cylinder with a grid of holes in it.

I'm using the following features in FreeCAD:

• Part View
  • Create and place cylinders
  • Shape actions on shapes (difference in this case)
  • Fillet (you also have chamfer)
• Draft View
  • Array toolArray tool
    • Polar array (circular)
    • Orthogonal array (linear)