Methods and systems for measuring a characteristic of a substrate or preparing a substrate for analysis are provided. One method for measuring a characteristic of a substrate includes removing a portion of a feature on the substrate using an electron beam to expose a cross-sectional profile of a remaining portion of the feature. The feature may be a photoresist feature. The method also includes measuring a characteristic of the cross-sectional profile. A method for preparing a substrate for analysis includes removing a portion of a material on the substrate proximate to a defect using chemical etching in combination with an electron beam. The defect may be a subsurface defect or a partially subsurface defect. Another method for preparing a substrate for analysis includes removing a portion of a material on a substrate proximate to a defect using chemical etching in combination with an electron beam and a light beam.