Wordpress is completely configurable given PHP skills so yes ... what do you want to do to your template?
I would like to take this opportunity to ask for some guidance here. I would like to tweak an existing 3 columns wordpress theme but do not have any idea. I've purchased Style Master but whenever I open the css file in Style Master, I can only see codes but not the layout. I have no coding knowledge and depends heavily on layout. Is there a way to do so? Thanks in advance.
A CSS file would not give you a layout, you would have to edit it manually. Just backup the original CSS code in a file and proceed with trial and error method, you will learn in a few days.
Have you tried using TopStyle? It at least gives a window at the bottom where you can view a sample output of whatever code you are writing. I've used only this so I don't know if others show the styles and formatting etc.