Although much is known about the molecular maternal-fetal interactions during implantation, the 3D architecture of the uterine environment in which the early embryo develops is not well understood. Using confocal imaging in combination with 3D analysis we identified dynamic changes in the luminal and glandular structure of the murine uterus in preparation for implantation. Further, we used this methodology to uncover patterns and mechanisms of pre-implantation embryo movement in the uterus. Our analysis reveals three distinct pre-implantation stages: a) Embryo entry; b) Unidirectional movement of embryo clusters; and c) Bidirectional scattering and spacing of embryos. We show that the unidirectional movement of embryo clusters is facilitated by a mechanical stimulus of the embryo as a physical object and is regulated by adrenergic uterine smooth muscle contractions. Surprisingly, we find that embryo scattering, is independent of muscle contractions but instead relies on LPAR3 signaling mediated embryo-uterine communication. Our data supports a model where murine uterine implantation sites are neither random nor predetermined and are a function of the number of embryos entering the uterine lumen. We propose that the presence of embryo clusters in the uterine horn provides an opportunity for the uterus to sense and count the embryos, followed by scattering and even spacing of these embryos along the given length of the horn. These studies have implications for understanding how embryo-uterine communication is key to determining an optimal implantation site, which is necessary for the success of a pregnancy.