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Material extrusion (ME) systems offer end-users with a more affordable and accessible additive manufacturing (AM) technology compared to other processes in the market. ME is often used to quickly produce low-cost prototyping with the freedom of scalability where parts can be produced in different geometries, quantities and sizes. As the use of desktop ME machines has gained widespread adoption, this review paper discusses the key design strategies and considerations to produce high quality ME parts, as well as providing actional advice to aid end-users in quickly identifying and efficiently troubleshooting issues since current information is often fragmented and incomplete. The systemic issues and solutions concerning desktop ME processes discussed are not machine-specific, covering categories according to printer-associated, deposition-associated and print quality problems. The findings show that the majority of issues are associated with incorrect printer calibration and parameters, hardware, material, Computer Aided Design (CAD) model and/or slicing settings. A chart for an overview of ME troubleshooting is presented allowing designers and engineers to straightforwardly determine the possible contributing factors to a particular problem.