File formats such as STL, PLY, and OBJ do not store the units of the coordinate system (i.e., whether the data is represented in millimeters, centimeters, inches, feet, etc.). For file formats the *do* store the units, like DICOM, Checkpoint automatically selects the appropriate setting whereas Checkpoint must guess for formats that do not store unit information.
There are a three places that control how landmark point coordinates/units are represented within Checkpoint. These should be set/reviewed in this order:
1) Set the units as stored in the data file by selecting from the menu "View | Specimen Units (per the file) | Millimeters, etc." This allows you to set the units of the data points stored within the specimen data file. To know this, you need to know what units were used within the software that wrote the data file. So, if you are using a laser scanner, that software will capture the scan in certain units (usually millimeters) and output according to those settings. You need to select the correct units as stored in the data file. If this option is greyed out, then the file you have loaded contains the correct unit information (such as DICOM) and Checpoint is using that setting. If this option is available, then the file format of the data does not store the units and you must check this option to ensure it is set correctly.
2) Set the display units from the menu option "View | Display Units | Millimeters, etc." This changes what units Checkpoint shows in its user interface. For example, your data may be stored in millimeters but you may want to see everything in centimeters - in which case you can select centimeters for the Display Units. You can see the difference by looking at the specimen data in the 3D window and looking closely at the measured extents of the gray bounding box around your data - if you don't see the gray bounding box you can turn it on from the menu "View | Show Bounding Box". This can be used as a sanity check for your data as the measurements reported here should accurately portray the size of your specimen.
3) Lastly, you can set the units used for exporting your data on the Export tab. Each section (Volume, Surface, and Landmarks) allows you to select the desired units for export giving you another chance to adjust the units prior to export.