A nano-scale metrology system, comprising: a substrate support assembly and a tip support assembly, each being supported by a base, the tip support assembly comprising a scanning probe microscopy tip that is coupled to a tip stage assembly via a tip cantilever, the substrate support assembly comprising a fixture configured to support a substrate; a patch (142, 144) that is disposed on at least one of the substrate support assembly and the base; an irradiation source configured and arranged to direct an incident irradiation onto the SPM tip; an irradiation detector configured and arranged to receive a sample irradiation from the SPM tip, the sample irradiation being caused by the incident irradiation; an actuator system operatively coupled to the nano-scale metrology system and configured to effect relative motion between the SPM tip and at least one of the irradiation source and the irradiation detector; the actuator system further configured to effect relative motion between the SPM tip and the fixture for transfer of at least one particle or debris from the substrate to the SPM tip; the actuator system further configured to move the SPM tip relative to the patch (142, 144) for transfer of at least one particle or debris from the SPM tip to the patch (142, 144), wherein the patch (142, 144) comprises a patch material that is sufficiently soft for mechanically lodging the at least one particle or debris into the patch material; and a controller operatively coupled to the actuator system and the irradiation detector, the controller being configured to: move the SPM tip from a location proximate to the substrate to a metrology location to receive a first signal from the irradiation detector, receive the first signal based on a first response of the irradiation detector to the sample irradiation, analyze the first signal to identify one or more material attributes of the at least one particle or debris on the SPM tip, and effect relative motion between the SPM tip and at least one of the irradiation detector and the irradiation source via the actuator system based on the first signal. a substrate support assembly and a tip support assembly, each being supported by a base, the tip support assembly comprising a scanning probe microscopy tip that is coupled to a tip stage assembly via a tip cantilever, the substrate support assembly comprising a fixture configured to support a substrate; a patch (142, 144) that is disposed on at least one of the substrate support assembly and the base; an irradiation source configured and arranged to direct an incident irradiation onto the SPM tip; an irradiation detector configured and arranged to receive a sample irradiation from the SPM tip, the sample irradiation being caused by the incident irradiation; an actuator system operatively coupled to the nano-scale metrology system and configured to effect relative motion between the SPM tip and at least one of the irradiation source and the irradiation detector; the actuator system further configured to effect relative motion between the SPM tip and the fixture for transfer of at least one particle or debris from the substrate to the SPM tip; the actuator system further configured to move the SPM tip relative to the patch (142, 144) for transfer of at least one particle or debris from the SPM tip to the patch (142, 144), wherein the patch (142, 144) comprises a patch material that is sufficiently soft for mechanically lodging the at least one particle or debris into the patch material; and a controller operatively coupled to the actuator system and the irradiation detector, the controller being configured to: move the SPM tip from a location proximate to the substrate to a metrology location to receive a first signal from the irradiation detector, receive the first signal based on a first response of the irradiation detector to the sample irradiation, analyze the first signal to identify one or more material attributes of the at least one particle or debris on the SPM tip, and effect relative motion between the SPM tip and at least one of the irradiation detector and the irradiation source via the actuator system based on the first signal. move the SPM tip from a location proximate to the substrate to a metrology location to receive a first signal from the irradiation detector, receive the first signal based on a first response of the irradiation detector to the sample irradiation, analyze the first signal to identify one or more material attributes of the at least one particle or debris on the SPM tip, and effect relative motion between the SPM tip and at least one of the irradiation detector and the irradiation source via the actuator system based on the first signal.