To evaluate the first implementation of a deconvolution algorithm in a commercial water phantom scanning software. Line dose profile measurements in a water phantom are an essential part of a quality assurance system and in base data measurements in radiotherapy. Usually these measurements are performed with waterproof ionization chambers of various sizes. These dose profile measurements are broadened by the Gaussian response functions of the detectors. In recent studies we showed that the undisturbed line dose profiles can be reconstruced by iterative deconvolution of the measured signal profiles with the Gaussian detector response functions. Recently, the proposed method was implemented in Mephisto 3.0. In this work we analyze the applicability and the limits of the deconvolution algorithm for several chambers by comparing the result with diode measurements. As long as the dose gradient becomes not too steep the deconvolution algorithm is able to reconstruct the undisturbed dose profiles with sufficient accuracy. Deviations occur for smallest field sizes in which the width of the detector's lateral response functions reaches the dimensions of the field. A simple chart for those limits is derived. The implemented deconvolution algorithm allows a fast and simple correction of measured dose profiles broadened by the volume effect of the ionization chambers. It offers therefore for the first time a clinical deconvolution of the profiles on a regular base and by this the implementation of undisturbed base data in the treatment planning systems as well as in the quality assurance process in modern radiotherapy.