After pasting in a structure from ChemDraw, the model does not look correct and/or I receive warnings in the Messages window.
Chem3D builds models according to the atom types defined in the Atom Types table. If an atom type is not defined, Chem3D will make a guess at the closest atom type available in the Atom Types table. You may need to define missing atom types. See the Chem3D manual for information on creating new atom types.
You may also want to adjust the Building Settings. Open the Chem3D Settings(consult your Chem3D manual for the location of the Settings/Preferences dialog box for your version of Chem3D) and try turning off the Apply Standard Measurements, Correct Atom Types, and Rectification Building Settings. After doing this, try pasting in your ChemDraw structure.