Systems, methods, and devices are provided for assisting or performing guided interventional procedures using custom templates. The system uses pre-procedure scans of a patients anatomy to identify targets and critical structures. A template is then manufactured containing guide elements. During a procedure, the template may be aligned to the patient and instruments passed though the guide elements and into various targets. The template may be aligned using one or more of, for example, a position sensing system or a live imaging modality to register the patient to the template. The system makes optional use of devices designed to immobilize or track an organ during therapy.