We used scanning white light interferometry to view the craters produced during secondary ion mass spectrometry (SIMS) analysis of the CaCO3 skeleton of an aragonitic coral. delta O-18, delta C-13 and delta B-11 analyses were determined. Sputtering rates were similar to 6 mu m(3)nA(-1)min(-1) for a delta O-16(-) primary beam and ranged from similar to 12 mu m(3)nA(-1)min(-1) (for delta O-18 analyses) to similar to 19 mu m(3)nA(-1) (for delta C-13 analyses) using a Cs+ primary beam. Sputter yields (atoms sputtered/impinging primary ions) ranged from 1.3 to 1.4 for a delta O-16(-) primary beam and from 2.5 to 4.5 using a Cs+ primary beam. Useful ion yields (ions detected/atoms sputtered), using instrument conditions typically used in geoscience applications, were of the order of 10(-4) for B, Mg, Ca, Sr, Ba and C and 10(-2) for O. delta C-13 analyses) to similar to 36 mu m (delta B-11 analyses) and crater depths range from 3 mu m (delta O-18 analyses) to >20 mu m (delta B-11 analyses). These dimensions are significant in relation to accretion rates in a range of biogenic carbonates and SIMS analyses typically sample carbonate deposited over time periods of days to months depending on the organism and structure analysed. In culture calibration studies, accurate determination of the temporal resolution of the analysed volume is crucial to ensure that the entire volume reflects the culture conditions and does not include carbonate deposited prior to introduction of the organism to the culture system. Copyright (C) 2013 John Wiley & Sons, Ltd.