Yes,  you can develop 3D application using JavaFX. Use case of JavaFX 3D includes:

* Inventory and Process Visualization
* Scientific and Engineering Visualization
* 3D Charting
* Mechanical CAD and CAE
* Medical Imaging
* Product Marketing
* Architectural Design and Walkthroughs
* Advanced User Experience
* Mission Planning
* Training
* Entertainment

3D libraries like "FXyz" can help you to build 3D application.
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