This paper introduces the methodology proposed by our group to model the biological soft tissues deformations and to couple these models with Computer-Assisted Surgical (CAS) applications. After designing CAS protocols that mainly focused on bony structures, the Computer Aided Medical Imaging group of Laboratory TIMC (CNRS, France) now tries to take into account the behaviour of soft tissues in the CAS context. For this, a methodology, originally published under the name of the Mesh-Matching method, has been proposed to elaborate patient specific models. Starting from an elaborate manually-built "generic" Finite Element (FE) model of a given anatomical structure, models adapted to the geometries of each new patient ("patient specific" FE models) are automatically generated through a non-linear elastic registration algorithm. This paper presents the general methodology of the Mesh-Matching method and illustrates this process with two clinical applications, namely the orbital and the maxillofacial computer-assisted surgeries.