High resolution scanning Hall probe microscopy has been used to study flux line pinning in a thin superconducting Pb film evaporated on top of an ordered array of ferromagnetic Co dots. After magnetisation along the easy axis, all the nanomagnets are seen to be in single domain magnetic states with dipole stray field distributions ( T> T c). Upon cooling through the critical temperature of the superconducting film at H=0, we observe strong screening of the dipole fields which we attribute to fluxoid quantisation. After field cooling, we find that flux lines are selectively pinned at poles with the opposite sign of field and ordered structures which are commensurate with the underlying pinning array are observed. Each pinning site appears to be capable of trapping at least two flux lines, and no evidence has yet been seen for interstitial vortices at low temperatures. Results will be compared with those from the disordered pinning system found naturally in Cu-rich epitaxial YBCO thin films. These typically contain micron-sized normal Cu-rich precipitates, which have a similar density to other artificially patterned systems. We show that the precipitates act as strong pinning sites close to T c, and also give rise to weak magnetisation peaks at average matching fields.