A system for analyzing a film and detecting a defect associated therewith includes a scanning probe microscope having a nanotube tip with a material associated therewith which exhibits a characteristic that varies with respect to a film composition at a location corresponding to the nanotube tip. The system also includes a detection system for detecting the material characteristic and a controller operatively coupled to the detection system and the scanning probe microscope. The controller configured to receive information associated with the detected characteristic and use the information to determine whether the film contains a defect at the location corresponding to the nanotube tip. The invention also includes a method of detecting a film composition at a particular location of a film or substrate. The method includes associating a material exhibiting a characteristic which varies with respect to a film composition with a nanotube tip of a scanning probe microscope and detecting the characteristic. The method then includes the step of determining a composition of a portion of the film using the detected characteristic.