Material Extrusion (MEX) currently stands as the most widespread Additive Manufacturing (AM) process, but part quality deficiencies remain a barrier to its generalized industrial adoption. Quality control in MEX is a complex task as extrusion performance impacts the consistency of mechanical properties and the surface finish, dimensional accuracy, and geometric precision of manufactured parts. Recognizing the need for early-stage process monitoring, this study explores the potential of integrating Laser Triangulation Sensors (LTS) into MEX/P manufacturing equipment for layer-wise 3D inspections. Using a double-bridge architecture, an LTS-based sub-micrometric inspection system operates independently from the manufacturing process, enabling comprehensive digitization and autonomous reconstruction of the target layer’s topography. Surface texture is then computed using standardized indicators and a new approach that provides insight into layer quality uniformity. A case study evaluating two alternative extruder head designs demonstrates the efficacy of this integrated approach for layer quality characterization. Implementing a generalized layer-wise procedure based on this integration can significantly mitigate quality issues in MEX manufacturing and optimize process parameter configurations for enhanced performance.