In this paper we present a method for numerical correction of phase images captured in a digital holographic microscopy (DHM) setup adapted to tomographic measurement of biological objects. The purpose of the correction is a removal of the object wave deformation associated with a fluid filled fiber capillary, which is used in DHM system to enable manipulation of a specimen. The proposed correction procedure is based on a simple concept of the phase subtraction, preceded by an estimation of the aberration profile using areas of a hologram that have not been affected by the object. The phase subtraction methodology, developed on the ground of the thin element approximation, is very effective in the visual enhancement of phase images; however, its application to quantitative measurement of micro-objects is questionable. Therefore, in this paper we verify the possible use of the phase subtraction methodology in DHM by performing a numerical experiment, supported with the finite difference time domain method (FDTD), which allows us to identify the residual error of the correction. The FDTD computation reveals that the phase subtraction methodology is insufficient to properly remove the influence of a capillary, in particular to compensate for two effects associated with the focusing properties of the aberration: a transversal shift of the image and the change of its magnification. Nevertheless, the possibility of the visual improvement of holographic images of a living human leukemia cell using the outlined method is demonstrated.