Observing dynamic micro-scale phenomena occurring at millisecond time scales, such as organism activity, micron particle flows, or any opaque object observation, requires volumetric microscopy techniques able to achieve high data acquisition rates while maintaining contrast so that measurement of fine micro-scale features is possible. In realizing this purpose, the light-field (LF) technique has already been used on three-dimensional (3D) scene capturing and even for microscopic visualizations. In studying the ability and feasibility of 3D surface morphology reconstruction via LF microscopy, we adopted a lab-made LF microscope and integrated a four-dimensional Fourier slice algorithm and a Markov random field propagation algorithm. Furthermore, for numerical comparison and quantized analysis, the Tenengrad function was utilized to calculate the average contrast of the region of interest. Reflective US Air Force targets and 3D photolithography-made micro-scaffolds coated with 50 nm nickel thin films were adopted for system alignment and calibration. The experimental results demonstrate that the developed LF microscope with the signal processing algorithms can observe the 3D surface morphology of opaque microstructures with one snapshot, and has been preliminary applied to Brownian motion observation with 30 Hz volumetric image rate.