Surface modification of MoSe2 has been accomplished in an electrochemical environment by a combined technique of scanning tunneling microscopy (STM) indentation with the following etching reaction. The artificial holes (defects), amde by STPYI indentation, could successfully serve as sites that initiated the electrochemical etching reaction that resulted in growth of the holes. The etching progressed in a highly anisotropic way, mainly occurring toward directions within the basal plane of the MoSe2, and predominantly leaving the step edges with equilateral triangular shapes. The etched holes had depths of a few van der Waals layers of the MoSe2, irrespective of the depths of the artificially made initial holes. The present technique could provide favorable opportunities not only for nanometer scale lithography in solution but also for fundamental studies on the mechanism of the etching processes at layered transition metal dichalcogenide materials.