A new automated technique for the estimation of the lateral calibration factors and for the drift in the fast scanning direction of SXM instruments is introduced. It is based on the detection of the reciprocal unit cell in Fourier space. The estimated calibration and drift factors are used for the restoration of distorted images containing self-assembled didodecylbenzene (DDB) molecules physisorbed on graphite. From the corrected images, the DDB unit cells are calculated in the Fourier domain. The long unit cell vector of the DDB molecules is calculated more accurately from images showing the graphite unit cells ’and the DDB lamellas simultaneously. By use of a correlation averaging technique, the structures of the DDB molecules within the unit cells are furthermore analyzed. The benzene ring and the C2H4 groups are thereby identified in the alkyl chains.