In the SEM vertical distances can not be directly measured from secondary electron intensity because there are many factors that impact the generation and efficient collection of secondaries. Vertical distances can be only determined using stereoscopic pairs or shadowing techniques.
Lateral distances can be measured directly from SEM images. While the SEM scan amplifiers are calibrated, an imaging resolution standard can be used to check the accuracy of the magnification. This image shows a series of horizontal and vertical 10 um pitch lines that can be used to check the lateral length calibration in two orthogonal dimensions. Many such structures are available on a test pattern at CMMP for the purpose of length calibration. These include longer "ruler" types of patterns that can be used to calibrate very long distance measurements.