This paper presents a novel method that utilizes multi-site and multi-probe capabilities of an ATE for testing of pre-assembly MCM substrates. Testing multiple SUTs (substrates under test) simultaneously can improve the efficiency of the probes in an ATE and considerably reduce the total test time. An analytical model that predicts very accurately the testing time of a SUT batch is proposed. Based on this model, the optimal multi-site testing configuration as corresponding to the batch size can be established. Simulation results for an ATE with 12 flying-probes as an example of a commercially available tester are provided; for this ATE the proposed method achieves a reduction of 54.66% in test time over a single-site method (both at complete coverage of the modeled faults).