We describe an open-source and widely adaptable Python library that recognizes morphological features and domains in images collected via scanning probe microscopy. π-Conjugated polymers (CPs) are ideal for evaluating the Materials Morphology Python (m2py) library because of their wide range of morphologies and feature sizes. Using thin films of nanostructured CPs, we demonstrate the functionality of a general m2py workflow. We apply numerical methods to enhance the signals collected by the scanning probe, followed by Principal Component Analysis (PCA) to reduce the dimensionality of the data. Then, a Gaussian Mixture Model segments every pixel in the image into phases, which have similar material-property signals. Finally, the phase-labeled pixels are grouped and labeled as morphological domains using either connected components labeling or persistence watershed segmentation. These tools are adaptable to any scanning probe measurement, so the labels that m2py generates will allow researchers to individually address and analyze the identified domains in the image. This level of control, allows one to describe the morphology of the system using quantitative and statistical descriptors such as the size, distribution, and shape of the domains. Such descriptors will enable researchers to quantitatively track and compare differences within and between samples.