Estimating clumping indices is important for determining the leaf area index (LAI) of forest canopies. The spatial distribution of the clumping index is vital for LAI estimation. However, the neglect of woody tissue can result in biased clumping index estimates when indirectly deriving them from the gap probability and LAI observations. It is difficult to effectively and automatically extract woody tissue from digital hemispherical photos. In this study, a method for the automatic detection of trunks from Terrestrial Laser Scanning (TLS) data was used. Between-crown and within-crown gaps from TLS data were separated to calculate the clumping index. Subsequently, we analyzed the gap probability, clumping index, and LAI estimates based on TLS and HemiView data in consideration of woody tissue (trunks). Although the clumping index estimated from TLS had better agreement (R2 = 0.761) than that from HemiView, the change of angular distribution of the clumping index affected by the trunks from TLS data was more obvious than with the HemiView data. Finally, the exclusion of the trunks led to a reduction in the average LAI by ~19.6% and 8.9%, respectively, for the two methods. These results also showed that the detection of woody tissue was more helpful for the estimation of clumping index distribution. Moreover, the angular distribution of the clumping index is more important for the LAI estimate than the average clumping index value. We concluded that woody tissue should be detected for the clumping index estimate from TLS data, and 3D information could be used for estimating the angular distribution of the clumping index, which is essential for highly accurate LAI field measurements.