Understanding the contact and friction between soft materials is vital to a wide variety of engineering applications including soft sealants and medical devices such as catheters and stents. Although the mechanisms of friction between stiff materials have been extensively studied, the mechanisms of friction between soft materials are much less understood. Time-dependent material responses, large deformations, and fluid layers at the contact interface, common in soft materials, pose new challenges toward understanding the friction between soft materials. This article aims to characterize the three-dimensional (3D) contact interfaces in soft materials under large deformations and complex contact conditions. Specifically, we introduce a microindentation and visualization (MIV) system capable of investigating soft material contact interfaces with combined normal and shear loading. When combined with a laser scanning confocal microscope, the MIV system enables the acquisition of 3D image stacks of the deformed substrate and the indenter under fixed normal and shear displacements. The 3D imaging data allows us to quantify the 3D contact profiles and correlate them with the applied normal and shear displacements. Using a spherical indenter and a hydrogel substrate as a model system, we demonstrate that the MIV system and the associated analysis techniques accurately measure the contact area under combined normal and shear loading. Although the limited speed of confocal scanning implies that this method is most suitable for quasi-static loading conditions, potential methods to increase the imaging speed and the corresponding trade-off in image resolution are discussed. The method presented here will be useful for the future investigation of soft material contact and friction involving complex surface geometries.