Collagen gels provide a versatile and widely used substrate for three-dimensional (3D) cell culture. Here we describe how cell-seeded Type-I collagen gels can be adapted to provide powerful 3D models to support a wide range of research applications where cell/substrate alignment, density, stiffness/compliance, and strain are critical factors. In their fully hydrated form, rectangular collagen gels can be tethered such that endogenous forces generated as resident cells attach to and remodel the fibrillar collagen network can align the substrate in a controllable, predictable, and quantifiable manner. By removing water from collagen gels (plastic compression), their density increases towards that of body tissues, facilitating the engineering of a range of biomimetic constructs with controllable mechanical properties. This dense collagen can be used in combination with other components to achieve a range of functional properties from controlled perfusion, or tensile/compressive strength to new micro-structures. Detailed methodology is provided for the assembly of a range of 3D collagen materials including tethered aligned hydrogels and plastic compressed constructs. A range of techniques for analysing cell behaviour within these models, including microscopy and molecular analyses are described. These systems therefore provide a highly controllable mechanical and chemical micro-environment for investigating a wide range of cellular responses.