A microwave ablation system configured for use in luminal network is provided. The microwave ablation system includes a microwave energy source. A tool for treating tissue is provided with the microwave ablation system. An extended working channel is configured to provide passage for the tool. A locatable guide catheter is positionable through the extended working channel and configured to navigate the extended working channel adjacent the target tissue. The microwave ablation system includes a navigation system that is configured for guiding the tool, extended working channel or the locatable guide through a luminal network following a predetermined determined pathway to the target tissue. One or more imaging modalities may be utilized for confirming placement of the tool within target tissue.