The paper presents the compliance errors compensation technique for over-constrained parallel manipulators under external and internal loadings. This technique is based on the non-linear stiffness modeling which is able to take into account the influence of non-perfect geometry of serial chains caused by manufacturing errors. Within the developed technique, the deviation compensation reduces to an adjustment of a target trajectory that is modified in the off-line mode. The advantages and practical significance of the proposed technique are illustrated by an example that deals with groove milling by the Orthoglide manipulator that considers different locations of the workpiece. It is also demonstrated that the impact of the compliance errors and the errors caused by inaccuracy in serial chains cannot be taken into account using the superposition principle.