Although 2D materials have been widely studied for more than a decade, very few studies have been reported on the in-plane structure domain (STD) size even though such a physical property is critical in determining the charge carrier and energy carrier transport. Grazing incidence X-ray diffraction (XRD) can be used for studying the in-plane structure of very thin samples, but it becomes more challenging to study few-layer 2D materials. In this work the nanosecond energy transport state-resolved Raman (nET-Raman) technique is applied to resolve this key problem by directly measuring the thermal reffusivity of 2D materials and determining the residual value at the 0 K-limit. Such a residual value is determined by low-momentum phonon scattering and can be directly used to characterize the in-plane STD size of 2D materials. Three suspended MoSe2 (15, 50 and 62 nm thick) samples are measured using nET-Raman from room temperature down to 77 K. Based on low-momentum phonon scattering, the STD size is determined to be 58.7 nm and 84.5 nm for 50 nm and 62 nm thick samples, respectively. For comparison, the in-plane structure of bulk MoSe2 that is used to prepare the measured nm-thick samples is characterized using XRD. It uncovers crystallite sizes of 64.8 nm in the (100) direction and 121 nm in the (010) direction. The STD size determined by our low momentum phonon scattering is close to the crystallite size determined by XRD, but still shows differences. The STD size by low-momentum phonon scattering is more affected by the crystallite sizes in all in-plane directions rather than that by XRD that is for a specific crystallographic orientation. Their close values demonstrate that during nanosheet preparation (peeling and transfer), the in-plane structure experiences very little damage.