The masterfeats.2da file is the .2da that defines groupings of feats that are treated as one when they are displayed for selection during level-up (and character creation). They tend to differ in some specialization, such as skill focus being a grouping of feats and skill focus (heal) being a specialization of that grouping. After a player selects one of these "master" feats, a specialized sub-feat is then chosen from a pop-up window. The information in this .2da generally only affects level-up, as at other times it would be the information about the sub-feats that is used.