Disclosed is a system and method for configuring control rules for applications executable on a computer. An example method includes classifying computer applications into one of a plurality of classification groups that include at least one predetermined classification group and an unknown classification group. The method further includes configuring control rules when the applications are classified in the unknown classification group that is done by determining, by the hardware processor, a computer competency score for a user of the computer; categorizing the applications into one or more predefined categories, and defining control rules for the application based on the determined computer competency score for the user and the one or more predefined categories of the at least one application.