This is pretty simple as this system allows you to save the STL files on your computer.  So, it’s a matter of simply uploading the files into the Doctor's Portal.

Just save the two files (upper and lower scan) on your desktop with the arches oriented in occlusion.  When you get to the step in the Doctor's Portal asking for PVS impression or scans, simply upload the files at this point into the Doctor's Portal.

Here are the steps visually laid out:

1. After you log in to the Lythos scanner, the “Case Setup” screen   appears. Enter all necessary information. Select “Digital Impressions”   at the bottom of the screen.

2. Perform the required System Check (if it’s the first scan of the day with   the scanner).

3. Scan the upper and lower arches. Make sure you capture at least 3-4 mm of distortion free gingival area adjacent to all of the teeth. The more accurate the scan, the better the aligners will turn out.

4. Capture a bite registration (either CR or CO bite).

5. After all of the digital scans are completed (upper arch, lower arch, bite   registration), select “complete impressions” at the bottom of the screen.

6. A confirmation screen appears; select “Yes” if you are satisfied with the digital impressions.

7. The impressions will be sent into the data transfer queue for transfer to digital storage.

8. Then go to ormcodigital.com, log in, and select the   “Patient Scans” tab located toward the middle of the page.

9. Find the patient that you want to submit to ClearCorrect, select   “Download,” a pop-up will appear and select “Download” and save the file to   your computer or drive.

10. Note that the patient’s scan will be saved on to your computer and labeled as “Upper_Arch” and “Lower_Arch” and it will include the bite   registration, even though it is not listed.

Note: ClearCorrect only requires the upper and lower arch scans because the positional data from the occlusal scan is embedded in the upper and lower files themselves. They know that some scanners generate three files, but since all the pertinent positional data is included in just the two, the third is not needed.

11. Log in to dr.clearcorrect.com 

12. Add the case and select your treatment options as usual.

13. Upload your STL files when you get to the "Impressions or Scans" step.