Metrology systems and methods are provided, which derive metrology target position on the wafer and possibly the target focus position during the movement of the wafer on the system's stage. The positioning data is derived before the target arrives its position (on-the-fly), sparing the time required in the prior art for the acquisition stage and increasing the throughput of the systems and methods. The collection channel may be split to provide for an additional moving-imaging channel comprising at least one TDI (time delay and integration) sensor with an associated analysis unit configured to derive wafer surface information, positioning and/or focusing information of the metrology targets with respect to the objective lens, during wafer positioning movements towards the metrology targets. Additional focusing-during-movement module and possibly feedbacking derived position and/or focus information to the stage may enhance the accuracy of the stopping of the stage.