Much Needed help!

I have a new version of illustrator. I'm not familiar with how it functions compared to my CS 5 that I once used . In the past I created line work with the pen tool but now I use the calligraphy brush tool on the same layer. I would  use the rectangle tool filled with whatever color I wanted to fill my line work. I would send the rectangle with color to the back , then I would select the line work and the rectangle filled work and hit the merge button in Pathfinder. I could then delete whatever colors. For example,  if the line work is of a portrait I'm working on I could remove the triangle fill color from inside the eyes etc and the filled rectangle would be trimmed off and fill the inside of my line work. This is not happening with the newest version of Ai. My line work disappears. Can someone please help me out with this issue I'm having or explain to me the newest way to achieve my goal? Thanks