This study investigated the effect of manufacturing parameters on the manufacturing quality of material extrusion additive manufacturing (MEAM), specifically focusing on the microscale geometry of lattice structures built up by discrete extruded filaments. The manufacturing parameters extrusion height, printing speed and extrusion width were investigated. Square grid structures, which can be precisely characterized, were used to develop fundamental understanding that can be translated to more complicated structures in future investigations. Print paths were directly created as machine control code (GCode) using FullControl GCode Designer, bypassing the conventional multi-stage translation of a design from CAD to an STL file, to slicing software and finally to GCode. This allowed precise parametric control of all aspects of the manufacturing procedure, including aspects that would not be possible with conventional slicing software such as control over the specific order and direction of printing each line, and the offsetting of specific printed lines on each layer in the Z direction by half the layer height. The printing quality of the structures was investigated with optical microscope and X-ray micro-computed tomography (micro-CT). Microscale changes to the extruded-filament geometry were characterized before and after filament-crossing points in the square grid structure, and internal cavities were identified. Printing speed was found to be a crucial parameter that should be carefully considered for lattice structure applications that require high manufacturing quality in terms of minimizing microscale geometric defects. Offsetting crossing extrudates by half the layer-height in the Z direction resulted in more consistent microscale geometry and greatly improved quality.