Methods and systems for heating a body tissue region adjacent a body lumen using selective accumulation of energy without knowledge of tissue topography. Methods include positioning an energy delivery portion of a catheter within the lumen adjacent the body tissue region, determining a pulse characteristic in response to a thermal property of a first tissue type and applying pulsed energy with the characteristic to treat a second tissue type within the region by drawing heat from the first tissue at a rate that inhibits thermal damage to the first tissue while building-up heat in the second tissue. Systems include a catheter body having an energy delivery portion processor configured to control a pulse characteristic of pulsed energy to therapeutically treat the second tissue by drawing heat from the first tissue at a rate that inhibits thermal damage to the first tissue while building-up heat in the second tissue.