As performance of van der Waals heterostructure devices is governed by the nanoscale thicknesses and homogeneity of their constituent mono-to few-layer flakes, accurate mapping of these properties with high lateral resolution becomes imperative. Spectroscopic ellipsometry is a promising optical technique for such atomically thin-film characterization due to its simplicity, noninvasive nature and high accuracy. However, the effective use of standard ellipsometry methods on exfoliated micron-scale flakes is inhibited by their tens-of-microns lateral resolution or slow data acquisition. In this work, we demonstrate a Fourier imaging spectroscopic micro-ellipsometry method with sub-5 μm lateral resolution and three orders-of-magnitude faster data acquisition than similar-resolution ellipsometers. Simultaneous recording of spectroscopic ellipsometry information at multiple angles results in a highly sensitive system, which is used for performing angstrom-level accurate and consistent thickness mapping on exfoliated mono-, bi-and trilayers of graphene, hexagonal boron nitride (hBN) and transition metal dichalcogenide (MoS 2 , WS 2 , MoSe 2 , WSe 2 ) flakes. The system can successfully identify highly transparent monolayer hBN, a challenging proposition for other characterization tools. The optical microscope integrated ellipsometer can also map minute thickness variations over a micron-scale flake, revealing its lateral inhomogeneity. The prospect of adding standard optical elements to augment generic optical imaging and spectroscopy setups with accurate in situ ellipsometric mapping capability presents potential opportunities for investigation of exfoliated 2D materials.