In this paper, a Finite Element-based surrogate model is developed to efficiently estimate stiffness properties of unidirectional composite laminas, while accounting for geometric and material property uncertainties at micro, meso and laminate scale, all within a probabilistic framework. In the multi-scale build-up nature of composites, uncertainties occur in material properties and geometric characteristics. These uncertainties present a challenge in estimating composite material properties. The currently available property estimation/homogenisation tools are mainly divided into two categories: analytical methods constrained by configuration assumptions, and numerical homogenisation using Finite Element Analysis (FEA). The latter is more flexible and accurate, but computationally expensive. Hence, this paper develops a surrogate model based on a limited number of experimental FEA data points. Additionally, a transition phase is developed between micro and laminate scales that enables modelling of spatially varying uncertainties. As a result, this framework significantly decreases analysis duration compared with FEA techniques, and, because it is derived from FEA data points, can accurately represent a wide range of uncertainties.