PeakForce quantitative nanomechanical AFM mode (PF-QNM) is a popular AFM technique designed to measure multiple mechanical features (e.g., adhesion, apparent modulus, etc.) simultaneously at the exact same spatial coordinates with a robust scanning frequency. This paper proposes compressing the initial high-dimensional dataset obtained from the PeakForce AFM mode into a subset of much lower dimensionality by a sequence of proper orthogonal decomposition (POD) reduction and subsequent machine learning on the low-dimensionality data. A substantial reduction in user dependency and subjectivity of the extracted results is obtained. The underlying parameters, or “state variables”, governing the mechanical response can be easily extracted from the latter using various machine learning techniques. Two samples are investigated to illustrate the proposed procedure (i) a polystyrene film with low-density polyethylene nano-pods and (ii) a PDMS film with carbon–iron particles. The heterogeneity of material, as well as the sharp variation in topography, make the segmentation challenging. Nonetheless, the underlying parameters describing the mechanical response naturally offer a compact representation allowing for a more straightforward interpretation of the high-dimensional force–indentation data in terms of the nature (and proportion) of phases, interfaces, or topography. Finally, those techniques come with a low processing time cost and do not require a prior mechanical model.