We have carried out surface photometry and an isophotal analysis for a sample of 25 early-type dwarf (dE and dS0) galaxies in the Virgo cluster based on CCD images taken at the VLT with FORS1 and FORS2. For each galaxy we present $B$ and $R$-band surface brightness profiles, as well as the radial colour ($B-R$) profile. We give total apparent $BR$ magnitudes, effective radii, effective surface brightnesses and total colour indices. The light profiles have been fitted with Sersic models and the corresponding parameters are compared to the ones for other classes of objects. The observed profiles of the brightest cluster dwarfs show significant deviations from a simple Sersic model, indicating that there is more inner structure than just a nucleus. In addition, we find a relation between the effective surface brightness, at a given luminosity, and the strength of the offset of the galaxys nucleus with respect to the center of the isophotes. Dwarfs with large nuclear offsets also tend to have stronger isophotal twists. In sum, our findings suggest the presence of substructure in most, and preferentially in the less compact, bright early-type dwarfs. The physical (dynamical) meaning of this has yet to be explored. (abridged)