Homebrew PCBs

I tried Eagle, I did a scematic in it then transfered it to the PCB 
program. I didnt like it as much as the program PCB express provides. 
But I could live with it. The one problem i could not figure out (not 
that I killed myself trying to fix it) when I printed a PC pattern, it 
printed parts outlines also, making the board pattern useless. Anyone 
have an answer for what was wrong?