We used scanning white light interferometry to view the craters produced during secondary ion mass spectrometry (SIMS) analysis of the CaCO skeleton of an aragonitic coral. The dimensions and volumes of craters sputtered during trace element, δO, δC and δB analyses were determined. Sputtering rates were ∼6 μm nA min for a O primary beam and ranged from ∼12 μm nA min (for δO analyses) to ∼19 μm nA (for δC analyses) using a Cs primary beam. Sputter yields (atoms sputtered/impinging primary ions) ranged from 1.3 to 1.4 for a O 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 for B, Mg, Ca, Sr, Ba and C and 10 for O. The maximum lengths of the SIMS craters, at the sample surface, range from ∼17 μm (δC analyses) to ∼36 μm (δB analyses) and crater depths range from ≤3 μm (δO analyses) to >20 μm (δB 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.