Disclosed are system and method for executing calls to a file system of a computer. An exemplary method comprises intercepting, by a software agent, a call to the file system; determining one or more parameters of the call that identify its functionality; determining a priority of executing the call based on the one or more parameters; storing information about the call, the parameters and the priority into a database; selecting from the database, one or more calls for execution based at least in part on relative priorities of execution of the plurality of calls stored in the database; determining whether to execute or not to execute a selected call based on whether the selected call interferes with execution of an earlier selected call; and when the selected call does not interfere with execution of an earlier selected call, passing the selected call to the file system for execution.