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I read a few posts here at GIS.SE that points to useful algorithms in CGAL. I'd like to test algorithms in CGAL such as medial axis transformation/polygon skeleton extraction, but the examples on the CGAL website are using text files or eps for input/output.

And I am just wondering what's the best way to use shapefiles and other common GIS formats in CGAL?

For example, can I convert polgon shapefiles to a common data format that CGAL reads/writes?

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You'll want to check out SFCGAL, a wrapper library for CGAL that exposes CGAL functionality in terms of OGC Simple Features. If you load your shapefiles into PostGIS, you can call many SFCGAL operations directly - there's a list in the PostGIS docs.

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