Atomic force microscopy, AFM, has been used for determining the microstructure of thermosetting matrices toughened by incorporation of core-shell particles and high-performance thermoplastics. A variety of systems has been considered in this work: one group is based on diglycidyl ether of bisphenol-A (DGEBA) epoxy matrix, and the other group is based on bisphenol-A dicyanate (DCBA) matrix. The studied epoxy systems were: DGEBA cured with an aromatic hardener, diamino diphenyl sulfone (DDS), and modified with polymethylmethacrylate (PMMA), or cured with a cycloaliphatic hardener, diamino dimethyl cyclohexylmethane (3DCM), and modified with core-shell particles of polystyrene-co-butylacrylate (PS-co-Bu). The DCBA-based matrices have been modified with polysulfone of bisphenol-A (PSU) or with polyetherimide (PEI). The influence of the modifiers and the curing conditions on the generated morphologies is reported as analysed by AFM in contact and tapping modes.