Variations in x-ray beam, filtration and detector gain characteristics are corrected by a multiple thickness flattening system. Preferably, an automatic multi-position attenuator mechanism inserts into the x-ray beam one or more flat reference attenuators of uniform composition. Thereafter, the response at each detector channel is measured. Unique factors are thus collected for each channel at multiple attenuation levels. An overall uniform response across the scan field is achieved by applying these correction factors to subsequent scan data. The current system compensates for detector gain by alternately turning X-rays on and off, so that dark level measurements can be interspersed with X-ray signal measurements. Detector offsets are eliminated in a linear data representation, while beam and detector flattening corrections are applied in a logarithmic data representation.