The native file formats for ChemDraw are the binary CDX and the preferred XML-based CDXML formats.
ChemDraw can also import from, and export to, MOL, SDF, and SKC chemical file formats.
Plugins
SDK for ChemDraw enables third-party developers to write plugins. For example, Quick HotKey helps to set up HotKeys in interactive mode instead of manually editing the text file.
The plugin website http://www.cambridgesoft.com/services/documentation/sdk/ appears to have been abandoned, and redirects to Revvity Signals' website.
Li, Z.; Wan, H.; Shi, Y.; Ouyang, P. (2004). "Personal Experience with Four Kinds of Chemical Structure Drawing Software: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch". J. Chem. Inf. Comput. Sci.44 (5): 1886–1890. doi:10.1021/ci049794h. PMID15446849.