Two-dimensional (2D) materials, such as graphene and metal dichalcogenides, are an emerging class of materials, which hold the promise to enable next-generation electronics. Features such as average flake size, shape, concentration, and density of defects are among the most significant properties affecting these materials' functions. Because of the nanoscopic nature of these features, a tool performing morphological and functional characterization on this scale is required. Scanning Probe Microscopy (SPM) techniques offer the possibility to correlate morphology and structure with other significant properties, such as opto-electronic and mechanical properties, in a multilevel characterization at atomic-and nanoscale. This review gives an overview of the different SPM techniques used for the characterization of 2D materials. A basic introduction of the working principles of these methods is provided along with some of the most significant examples reported in the literature. Particular attention is given to those techniques where the scanning probe is not used as a simple imaging tool, but rather as a force sensor with very high sensitivity and resolution.