Integrating computational tasks in coordinate metrology and its effect on the inspection’s uncertainty is studied. It is shown that implementation of an integrated inspection system is crucial to reduce the uncertainty in minimum deviation zone (MDZ) estimation. An integrated inspection system based on the iterative search procedure and online MDZ estimation is presented. The search procedure uses the Parzen Windows technique to estimate the probability density function of the geometric deviations between the actual and substitute surfaces. The computed probability density function is used to recognize the critical points in the MDZ estimation and to identify portions of the surface that require further iterative measurements until the desired level of convergence is achieved. Reduction of the uncertainty in the MDZ estimation using the developed search method compared to the MDZ estimations using the traditional sampling methods is demonstrated by presenting experiments including both actual and virtual inspection data. The proposed search method can be used for assessing any geometric deviations when no prior assumptions about the fundamental form and distribution of the underlying manufacturing errors are required. The search method can be used to inspect and evaluate both primitive geometric features and complicated sculptured surfaces. Implementation of this method reduces inspection cost as well as the cost of rejecting good parts or accepting bad parts.