Material Extrusion (ME) offers end-users a more affordable and accessible Additive Manufacturing (AM) technology in contrast to other processes. ME is frequently used to quickly produce low-cost prototypes with the freedom of scalability where parts can be produced in various geometries, quantities and sizes. This article provides guidelines and advice for end-users to identify and efficiently troubleshoot issues concerning desktop ME processes quickly. The systemic issues and solutions covered include three categories: printer-related, deposition-related and quality problems. The majority of issues encountered in ME are associated with incorrect printer calibration and parameters, hardware, material, Computer-Aided Design (CAD) model and/or slicing errors. A troubleshooting chart for ME is presented that allows designers and engineers to determine the possible contributing factors for a particular problem in an efficient manner.