Surface roughness and texture are critical to the functional performance of engineering components. The ability to analyze roughness and texture effectively and efficiently is much needed to ensure surface quality in many surface generation processes, such as machining, surface mechanical treatment, etc. Discrete Wavelet Transform (DWT) and Discrete Cosine Transform (DCT) are two commonly used signal decomposition tools for surface roughness and texture analysis. Both methods require selecting a threshold to decompose a given surface into its three main components: form, waviness, and roughness. However, although DWT and DCT are part of the ISO surface finish standards, there exists no systematic guidance on how to compute these thresholds, and they are often manually selected on case by case basis. This makes utilizing these methods for studying surfaces dependent on the user's judgment and limits their automation potential. Therefore, we present two automatic threshold selection algorithms based on information theory and signal energy. We use machine learning to validate the success of our algorithms both using simulated surfaces as well as digital microscopy images of machined surfaces. Specifically, we generate feature vectors for each surface area or profile and apply supervised classification. Comparing our results with the heuristic threshold selection approach shows good agreement with mean accuracies as high as 95\%. We also compare our results with Gaussian filtering (GF) and show that while GF results for areas can yield slightly higher accuracies, our results outperform GF for surface profiles. We further show that our automatic threshold selection has significant advantages in terms of computational time as evidenced by decreasing the number of mode computations by an order of magnitude compared to the heuristic thresholding for DCT.