The objective of this work is to test whether (a) intra-grain boundaries in Cu are coherent twin boundaries, and (b) grain boundary scattering remains the dominant mechanism for resistivity increase and the simple addition of FS and MS resistivities is remains the best description for the resistivity size effect in Cu when the intra-grain boundaries are included for the grain size calculation. To characterize the grain boundaries at the scale of size effect samples, a newly developed orientation mapping technique in the transmission electron microscope (TEM) that combines precession microscopy with automated nanoprobe diffraction is employed. In this method, spot diffraction patterns from the specimen are collected by scanning a nanosized electron beam in the TEM. The incident beam is precessed about the optic axis to reduce the dynamical effects. Automated indexing of spot diffraction patterns is achieved by matching the observed spot pattern with a precalculated diffraction pattern using a template matching algorithm. Crystal orientation maps collected using this method from two Cu thin films (36.9 and 46.4 nm thick) that were used in the work of (Sun, Yao, Warren, Barmak, Toney, Peale and Coffey 2010) is presented. Analysis of these orientation maps shows that the intra-grain boundaries are Σ3 boundaries of which approximately 45% by length are coherent Σ3 boundaries. These orientation maps were then used to calculate the mean intercept length grain size with and without excluding Σ3 boundaries. The ratio of these two grain sizes is used as a conversion factor to convert the average grain sizes reported in Sun et al. (2010) to include the intra-grain boundaries. Application of these grain size calculations to the study of the resistivity size effect shows that the contribution from grain boundary scattering is still dominant compared to surface scattering towards resistivity increase. The resistivity data is best described by the combined FS and MS model using the Matthiessen's rule with a grain boundary reflection coefficient 0.26±0.01 and a surface specularity coefficient 0.50 (+0.00/-0.02).