Enzymatically modified starch granules are useful in the food industry by endowing improved thermal properties, resistance to digestion and complexation capacity. However, it is of interest to correlate structural features on the granular surface with functional characteristics relevant to given applications. To meet this requirement, a method was developed to quantify the density of α-1,6 branch points on differently structured starch granules as based on interfacial enzyme catalysis. The branch points are attacked by pullulanase, a debranching enzyme, and the branch point density, as calculated from the kinetic attack site density (^kinΓ_max), was linked to the chain length distribution (CLD) of the released segments. The procedure involved a combination of conventional and inverse Michaelis–Menten (MM) kinetics for pullulanase degradation of native, branching enzyme- or 4-α-glucanotransferase-modified granular waxy and normal maize starch (WMS and NMS). The treatment by branching enzyme increased the branch point density for WMS from 1.7 to 3.3 nmol/g starch granules. CLD analysis indicated that 4-α-glucanotransferase catalyzed hydrolysis and/or cyclization on the surface of the granules, rather than disproportionation. The CLD data reflected the different spatial organization of amylopectin chains within WMS and NMS granules related to their different amylose contents of 0.7 and 20.7%, respectively. Scanning electron microscopy confirmed that the starch granules retained the morphology without prominent cracks or pores after pullulanase hydrolysis for the analysis of interfacial kinetics. Comparison with the corresponding gelatinized starches gave new insights into the connection between substrate structure and specificity of the two glucotransferases acting on the different starches.