The soft x-ray diagnostic system of Alcator C-Mod, equipped with 152 detectors distributed in four arrays, is used to obtain iso-emissivity surfaces. These surfaces have been characterized by giving their elongation and relative shift from the centre of the tokamak as functions of plasma radius. Flux surfaces, provided by magnetic diagnostics, have also been described with elongation and shift. Results from the comparison of the two sets of geometric parameters obtained from magnetic and x-ray diagnostics are presented. We find that, whereas the shifts obtained from these two diagnostic methods are always in good agreement, the corresponding elongation curves show different patterns. An agreement between elongations better than 2% is only found in a range of about 2 cm in minor radius. On the other hand, the elongations can differ by 10% towards the plasma edge and the plasma centre. Error bars for the x-ray diagnostic are obtained by propagating the effect of random errors at the detector signals, and can amount to of the estimated values near the edge and the centre of the plasma. The estimated uncertainties in the determination of elongation from magnetic flux surfaces are of the order of 4%. A series of tests and simulations performed to verify the accuracy of the x-ray diagnostic system is presented. The discrepancies found could imply the existence of asymmetries in impurity concentration.