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The author defined for each (commutative) Frobenius algebra a skein module of surfaces in a $3$-manifold $M$ bounding a closed $1$-manifold $α\subset \partial M$. The surface components are colored by elements of the Frobenius algebra. The modules are called the Bar-Natan modules of $(M,α)$. In this article we show that Bar-Natan modules are colimit modules of functors associated to Frobenius algebras, decoupling topology from algebra. The functors are defined on a category of $3$-dimensional compression bordisms embedded in cylinders over $M$ and take values in a linear category defined from the Frobenius algebra. The relation with the $1+1$-dimensional topological quantum field theory functor associated to the Frobenius algebra is studied. We show that the geometric content of the skein modules is contained in a tunneling graph of $(M,α)$, providing a natural presentation of the Bar-Natan module by application of the functor defined from the algebra. Such presentations have essentially been stated previously in work by the author and Asaeda-Frohman, using ad-hoc arguments. But they appear naturally on the background of the Bar-Natan functor and associated categorical considerations. We discuss in general presentations of colimit modules for functors into module categories in terms of minimal terminal sets of objects of the category in the categorical setting. We also introduce a $2$-category version of the Bar-Natan functor, thereby in some way Bar-Natan modules of $(M,α)$.