Using the electron beam (e-beam) as an advanced metrology tool in semiconductor manufacturing technologies has attracted many interests in the recent years. Owing to its high resolution and transparency to a wide range of materials including the metals, the e-beam shows a great promise to be used individually or in combination with the current optical metrology techniques in semiconductor industries. However, the e-beam can cause damages to the materials under inspection due to its relatively high energy. Therefore, determining the amount and type of damage as a result of the e-beam exposure is critical. Here, we present scanning probe microscopy techniques with the capability of measuring the e-beam induced damages on various materials. The experimental results of the e-beam induced damages on 300 mm silicon wafers covered by 1) patterned low-k material and 2) patterned low-k material filled with copper metal after chemical-mechanical polishing treatment are discussed. This method can be considered as a complementary approach to e-beam to ensure minimizing damage to the features.