A hardware system is disclosed for detecting alignment marks on a substrate in connection with electron beam lithography. The system is considerably faster than prior software approaches. A scanning signal derived from backscattered electrons as the beam scans the substrate is stored and updated in a set of shift registers as scanning proceeds. The signals in the scanning shift registers are compared with a predetermined reference signal, corresponding to the expected scanning signal when the beam traverses an edge of an alignment mark, stored in another set of shift registers. A correlation is obtained between the scanning and reference signals by multiplying the values of the corresponding cells in the scanning and reference registers, and accumulating and weighting the result. The locations of the maximum positive and negative correlations, and hence the locations of the opposed edges of the alignment mark, are obtained by means of a timing mechanism coordinated with the scanning.