Despite tremendous progress of quantum computation with superconducting qubits, up-scaling for practical applications is hindered by decoherence and fluctuations induced by material defects. In this work, a qubit interface has been developed to study the microscopic nature of individual defects in a probe material. Further, a portable method has been developed to find locations of individual defects in ready-made qubit samples, which offers to test and improve micro-fabrication of qubits.