We prove the existence of resolution of singularities for arbitrary (not necessarily reduced or irreducible) excellent two-dimensional schemes, via permissible blow-ups. The resolution is canonical, and functorial with respect to automorphisms or etale or Zariski localizations. We treat the embedded case as well as the non-embedded case, with or without a boundary, and we relate the diferent versions. In the non-embedded case, a boundary is a collection of locally principal closed subschemes. Our main tools are the stratifications by Hilbert-Samuel functions and the characteristic polyhedra introduced by H. Hironaka. In an appendix we show that the standard method used in characteristic zero - the theory of maximal contact - does not work for surfaces in positive characteristic (the counterexamples are hypersurfaces in affine threespace and work over any field of positive characteristic).