There is much controversy about the optimal trade-off between blood-oxygen-level-dependent (BOLD) sensitivity and spatial precision in experiments on brain's topology properties using functional magnetic resonance imaging (fMRI). The sparse empirical evidence and regional specificity of these interactions pose a practical burden for the choice of imaging protocol parameters. Here, we test in a motor somatotopy experiment the impact of fMRI spatial resolution on differentiation between body part representations in cortex and subcortical structures. Motor somatotopy patterns were obtained in a block-design paradigm and visually cued movements of face, upper and lower limbs at 1.5, 2, and 3 mm spatial resolution. The degree of segregation of the body parts' spatial representations was estimated using a pattern component model. In cortical areas, we observed the same level of segregation between somatotopy maps across all three resolutions. In subcortical areas the degree of effective similarity between spatial representations was significantly impacted by the image resolution. The 1.5 mm 3D EPI and 3 mm 2D EPI protocols led to higher segregation between motor representations compared to the 2 mm 3D EPI protocol. This finding could not be attributed to differential BOLD sensitivity or delineation of functional areas alone and suggests a crucial role of the image encoding scheme - i.e., 2D vs. 3D EPI. Our study contributes to the field by providing empirical evidence about the impact of acquisition protocols for the delineation of somatotopic areas in cortical and sub-cortical brain regions.