The main ionospheric trough (MIT) is a salient density feature in the mid-latitude ionosphere and characterizing its structure is important for understanding GPS and HF signal propagation, and identifying geospace phenomena such as the plasmapause boundary layer. While a number of previous studies have statistically investigated the properties of the MIT utilizing low-altitude satellite observations, they have been limited to latitudinal cross sections, and have not considered the inherent two-dimensional structure of the trough. In this work, we develop a regularized inversion method for identifying the two dimensional structure of the trough in Total Electron Content (TEC) maps. Because no ground truth labels exist for the MIT, we extensively characterize the behavior of the algorithm by comparing it to the method developed by \citeA{aa-2020}. We show that statistics computed on the resulting labels are robust to our choice of algorithm parameters and that we are able to match the results of \citeA{aa-2020} with a particular selection of the parameters. Without ground truth, these two properties provide much stronger verification than a comparison using a single parameter setting. In addition to enabling fundamentally different studies, our MIT labels are able to provide statistical MIT properties with higher resolution.