We present a three-dimensional microscopic technique based on simultaneous dual wavelength digital holography. In digital holographic microscopy, interference patterns produced by an object and reference waves are recorded by a camera. The computationally reconstructed holographic images contain the information about both amplitude and phase of the light reflected from the object. Phase is then mapped across the sample and converted into height information for each pixel. This technique was applied to imaging of electrodes embedded into glass substrates, which allowed three-dimensional reconstruction of their structure. Holographic imaging of the embedded layered structures, where each layer can be separated from the others by axial distances exceeding multiple wavelengths of imaging light, is difficult, because software phase unwrapping is practically impossible. The use of two wavelengths enables accurate axial measurements of multiple layers by comparing the phase maps produced by each individual wavelength. We demonstrated that the correct choice of wavelengths maximizes the axial range, at which an unambiguous 3D imaging can be performed. This provides not just three-dimensional structure of each layer, but also allows for height differentiation of layers. By employing wavelength cutoff filters, we were able to obtain the phase maps simultaneously, enabling fast measurements. We also developed a background removal technique, based on the quality of interference fringe pattern, which suppresses low intensity signal when no reliable phase information can be extracted. We showed that this is especially useful for multilayered embedded electrode structures, where each sample consists of both high and low reflectivity features.