PETG and Clear Aligner? There is a material called PETG. In addition, there is a medical solution called Clear Aligner to fix perplexed teeth.
Can I use a 3D printer using PETG and make transparent apparatus?
The program I use gives transparent apparatus, 3-dimensional output in STL format. Do I get results if I send the STL file to the printer?
No
PETG is a material that can only be used in FDM machines. This precludes any internal medical use, as FDM prints can't be made sterile or even hygienic - the sterilization processes would destroy the print, and FDM layers create many spots for germs to grow. Atop that, you can't get the needed precision with FDM - which means any FDM prints are at best waste at worst endangering the patient!
In contrast, 3D printed metals and laser-printed nylon can be created and post-processed in ways that do not have layer lines. Resin prints do not have layer lines that offer these discrete hiding spots for germs. They all are made in a fashion that kills germs or disallows them from being embedded and they can be properly sterilized or made hygienic.
No!
PETG can't be printed completely clear in FDM. By the processing method, air and layer boundaries are included, making prints at least somewhat opaque.
Only Resin prints can be fully transparent as they contain neither boundaries nor air.
NO!!!
STL files contain only surface data and need to be processed into printer readable format. G-code is one of those formats, commonly used in FDM machines and CNC machines.
The processing from STL or other surface data into FDM-3D-printer G-code is done by a program called a slicer. Examples are Cura, PrusaSlicer, Slic3r, and many others.
Resin printers using DLP use different slicers that create images of the model's crossections together with some sort of machine code for the movement. For SLA machines, the code is entirely different again.
Further Reading
I highly suggest you read more about 3D printing dental applications before trying anything for dental use, and especially anything that is printed for any medical application!