This master's thesis describes the design and implementation of system for processing application protocols in high-speed networks using the concept of Software Defined Monitoring. The proposed solution benefits from hardware accelerated network card performing pre-processing of network traffic based on the feedback from monitoring applications. The proposed system performs pre-processing and filtering of network traffic which is handed afterwards passed to application modules. Application modules process application protocols and generate metadata that describe network traffic. Pre-processing consists of parsing of network protocols up to the transport layer, TCP reassembling and forwarding packet flow only to modules that are looking for a given network traffic. The proposed system closely links intercept related information internal interception function (IRI-IIF) and content of communication internal interception function (CC-IIF) to minimize the performing of duplicate operations and increase the efficiency of the system.