Antivirus blocked sistem

Hello, when I turn antivirus (Nod 32) for full scaning, the program ranning antil 93 % and stops when scan a My computer/Program file/...win 32/system.exe and blocked the all system and i must restart.
This problem start after I had a problem with Generic host prosces pops up. One of solution was to erase all the system 32 files with unknowen ending. Well the computer is running good, but antivirus ( I try with Avira as well) never finished then job and blocked.