What your going to want to do is create a plugin that uses WordPress filter and action hooks to remove features for people with particular user permissions. Here are some links for more info on this:
You might want to look into the Members plugin: http://wordpress.org/extend/plugins/members/ It's not going to help remove features directly, but it will help manage what particular users can do. Together with a plugin that assigns features to particular capabilities, you can get the results you want.
Could you explain further what features you want to remove. It's hard to describe what you should do if we don't know what you really want the final product to look like. Removing some features or functionality is going to be easier or harder than others.
Feel free to ask questions about anything you don't understand or want guidance with, e.g. finding where code is located or hooks that can modify a particular feature.
 Just to expand a little bit more just in case... In general it's a bad idea to modify code that your not the author of, because updates to WordPress, themes, or plugins will over write your changes. The best bet is to separate modifications from the original code using extensions, such as a plugin.