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This paper is devoted to the construction and analysis of immersed finite element (IFE) methods in three dimensions. Different from the 2D case, the points of intersection of the interface and the edges of a tetrahedron are usually not coplanar, which makes the extension of the original 2D IFE methods based on a piecewise linear approximation of the interface to the 3D case not straightforward. We address this coplanarity issue by an approach where the interface is approximated via discrete level set functions. This approach is very convenient from a computational point of view since in many practical applications the exact interface is often unknown, and only a discrete level set function is available. As this approach has also not be considered in the 2D IFE methods, in this paper we present a unified framework for both 2D and 3D cases. We consider an IFE method based on the traditional Crouzeix-Raviart element using integral values on faces as degrees of freedom. The novelty of the proposed IFE is the unisolvence of basis functions on arbitrary triangles/tetrahedrons without any angle restrictions even for anisotropic interface problems, which is advantageous over the IFE using nodal values as degrees of freedom. The optimal bounds for the IFE interpolation errors are proved on shape-regular triangulations. For the IFE method, optimal a priori error and condition number estimates are derived with constants independent of the location of the interface with respect to the unfitted mesh. The extension to anisotropic interface problems with tensor coefficients is also discussed. Numerical examples supporting the theoretical results are provided.