A method of operating a probe-based instrument includes providing a probe assembly and a probe holder and oscillating a probe of the probe assembly with an actuator that generates oscillation energy. The method also includes mounting the probe assembly on the probe holder so as to lessen interference with the oscillation energy coupled to the tip of the probe. A corresponding probe assembly includes a base having two substantially opposed surfaces and a cantilever extending from the base and supporting a tip. The probe assembly is mounted in a probe holder such that a probe holder surface contacts one of the opposed surfaces. The one opposed surface preferably includes at least one opening such that the surface area of the one opposed surface is substantially less than the surface area of the probe holder surface.