A method is for processing a plurality of finger biometric enrollment data sets that accounts for uncertainty in alignment between finger biometric enrollment data sets. The method may include generating a respective estimated physical transformation between each pair of finger biometric enrollment data sets, and generating a respective uncertainty for each estimated physical transformation. The method may also include associating the respective estimated physical transformation and the uncertainty for each estimated physical transformation with each pair of finger biometric enrollment data sets to define a logical finger biometric enrollment graph. The logical finger biometric enrollment graph is readily used for subsequent accurate matching in either touch sensor applications or slide sensor applications.