Nowadays, the multi-scale modelling of wood has a great need for measurements of structural, chemical and mechanical properties at the lowest level. In this paper, the viscoelastic properties in the layers of a wood cell wall are investigated using the contact resonance mode of an atomic force microscope (CR-AFM). A detailed experimental protocol suitable for obtaining reproducible and quantifiable data is proposed. It is based on three main steps: sample preparation to obtain a good surface state, calibration of the contact modulus using reference samples, and image processing to produce the viscoelastic images. This protocol is applied on chestnut tension wood. The obtained topography and semi-quantitative viscoelastic maps are discussed with respect to the cell wall structure, sample preparation effects, and AFM measurement specificity compared with nanoindentation.