The controlled modification of nanometer-size structures generated with the tip of a scanning tunneling microscope (STM) is demonstrated on the surface of the layered semiconductor tungsten diselenide (WSe4). Tn addition, the dependence of the apparent height of the structures on the tunneling voltage during imaging is investigated. For this purpose small hill structures with radii of about 1.5 nm were generated by applying voltage pulses of 3.2 V in amplitude between the STM lip and the sample at predefined locations. After this writing process and subsequent imaging, the hill structures were selectively manipulated with the tip of the STM. As a result, the apparent height of the structures was reduced while their diameter was increased by a factor of 1.5. By repeating the process, hill structures generated by voltage pulsing could be erased. Even after these operations, the STM images showed a preserved atomic order of the surface. While these experiments demonstrate tip-induced reshaping and erasure of the structures, a pronounced dependence of their height on the tunneling voltage (with variations between 4 Angstrom and 12 Angstrom) indicates a local modification of the electronic structure.