Method and system for protecting computer system from malicious software operation

A method and system for protecting a computer system from malicious software operations in real-time is disclosed. The security system combines system and user activity information to derive a user initiation attribute indicating whether or not a system operation is initiated by a computer user, and stop secrete malicious software operations that are not initiated by a computer user. The security system incorporates a plurality of attributes to support flexible security policy design, warn about potentially damaging operations by Trojan programs, and dynamically create security policies to allow trusted programs to perform trusted operations.