Atomic force microscopy (AFM) is used for measuring nano-scale topographic features. By exciting a micro-cantilever with a sharp stylus at its tip, at or near resonance, a Frequency Modulated AFM (FM-AFM) device can sense the change of resonance frequency due to the change in tip-surface Van der Waals (VdW) potential. The topography is then retrieved from the relationship between the potential and the distance between stylus and the specimen. To improve the measurement speed and address complex geometries emerging in industrial microchip constructions, several enhancements are introduced. While most FM-AFM devices operate in a single vibrating mode, this article enhances existing sensing methods by extending to multidimensional sensing the resonance frequencies that are modulated by the topology, in several orthogonal vibration modes simultaneously. The latter opens new possibilities, e.g. to measure steep walls and trenches or other complex geometries. An Autoresonance (AR) control scheme for faster excitation, and fast frequency estimation algorithm were used for sensing several modes simultaneously, without the need to wait for steady state settling of the cantilever. The concept was tested on a large-scale experimental system, where VdW forces between tip to surface were replaced by magnetic forces, using a magnetic tip and ferromagnetic samples. Experimental results employ 3D relevant topographies such as inclined surfaces, steep walls and trenches that were reconstructed experimentally with 4 (µm) resolution or better. Downscaling to typical AFM dimensions would theoretically yield sub-nanometer resolution. Numerical and experimental data are shown to demonstrate the advantageous of the new approach.