This paper presents a finite element (FE) embedding mesh technique to efficiently embed arbitrary fluid mesh patches into Cartesian or unstructured background fluid grids. Our motivating application for such a technique is to efficiently resolve flow features like boundary layers around structures, which is achieved by attaching fluid boundary layer meshes around these structure surfaces. The proposed technique can be classified as a non-overlapping domain decomposition method. The particular feature is that the embedded patch cuts a void region into the background grid independently of background element edges. Since the embedded fluid domain ends in the middle of background elements, extended FE techniques are used to model a sharp separation between active and inactive regions on the background grid. The active background region is coupled to the boundary layer mesh using a mixed/hybrid Lagrange multiplier technique as proposed in Gerstenberger and Wall (textitInt. J. Numer. Meth. Engng. 2010; 82:537–563). The coupling formulation works without stabilization for the Lagrange multiplier unknowns and the Lagrange multiplier can be completely condensed on the element level. Within this paper, the approach is derived for incompressible, viscous flows. Three-dimensional examples using linear and quadratic shape functions demonstrate the correctness and the versatility of the proposed approach. Copyright © 2010 John Wiley & Sons, Ltd.