Although additive manufacturing (AM) offers a reduction in waste compared to conventional manufacturing processes, AM still generates non-negligible material losses and inefficiencies, from print failures to removable support structures. This research aims to propose a systematic Material Flow Analysis (MFA) framework tailored for AM laboratories. As a comprehensive approach, the framework maps the complete operational process from the filament to the final printed product, rather than focusing on specific printing activities. The case study is the Fused Filament Fabrication division of the Laboratory for Multiscale Mechanics (LM2 ) at Polytechnique Montreal. LM2 is dedicated to 3D printing polymers and composites using commercial printers and filaments. The MFA will be classified into two flow categories: fixed and variable waste. Printed products are highly customizable, which distinguishes their waste management strategies from traditional manufacturing operations. Fixed waste, such as disposable gloves and cleaning wipes, is quantifiable and repeatable in each production cycle. Therefore, the framework proposes direct alternatives (reuse/replace), depending on the CO2 eq. emission tradeoff. Variable waste, such as support structures, is design-dependent and varies based on the product. In laboratory-scale production, eco-design principles are non-systematic, and different user experience levels complexify their implementation. Therefore, as an alternative systematic approach, the framework proposes mechanical recycling as a key strategy that is assessable based on CO2 eq. emission and adaptable to different design outputs. Overall, the MFA aims to offer a guideline for waste management flow for a customizable manufacturing method at laboratory scale, identifying potential pathways towards a sustainable AM industry.