1. A method for debugging a target application having potential malware, the method comprising triggering a System Management Interrupt (SMI) by a server, on receiving a triggering message from a client; entering a System Management Mode (SMM) by the server, on receiving at least one debugging command from the client, wherein interrupts handled by an operating system are disabled upon entry into the SMM, and wherein a subsequent SMI is configured by using a performance counter of the server; executing debugging commands on the target application by the server in SMM, wherein the server receives the debugging commands from the client, the debugging commands being executed within the SMI handler to make operation of the server transparent to the target application and underlying operating system; and sending a response message by the server to the client, the response message including information requested by a debugging command to debug the target application.