On a grammar note you want to be careful how you spell filling and filing, because they are both modelling techniques.
If you were getting good results with your knife, I would continue doing it that way. Most modelling techniques improve through practice. You are usually better off doing something where you are confident in your skill.
Metal files can be a fairly tough tool to use on plastic. A better method is to use a very fine type of sandpaper called 'wet and dry' paper.
http://en.wikipedia.org/wiki/Sandpaper
I use knife edge, files, disposable nail files and wet and dry paper as required depending on the amount of extra material I need to remove.
Your filing scratches may disappear under paint if they are very shallow. If you are worried they will show through, you can fill them with a modelling putty such as Tamiya or Milliput. Green stuff isn't useful for this because its texture is wrong.
You kind of 'swipe' a thin film of soft putty over the scratches, let it dry, then sand gently with fine 'wet and dry'.
A lot of people use side cutters for snipping the parts off sprues.