In one aspect, the invention relates to a method of acquiring optical coherence tomographic data from a sample. The method includes the steps of scanning a first location on the sample to obtain a first set of optical coherence tomographic data, scanning a second location on the sample to obtain a second set of optical coherence tomographic data, and defining a fiducial position relative to a location on the sample using one of the two sets of optical coherence tomographic data. In one embodiment, the first set of optical coherence tomographic data is survey data. However, in another embodiment the first set of optical coherence tomographic data is sample measurement data.