PIV restricts manipuli to mean either "wield or operate with the bare hands" or "guide or alter clandestinely" but my impression is that it is nowadays used in pretty much exactly the same way as the English word manipulate.
The translators for the GNU Image Manipulation Program chose to call it a bildmanipulilo. You can browse the translation here. More generally, however, I think any program to edit files is called a redaktilo, so an image editor is a bildoredaktilo. A retouched photo is a retuŝita foto. A modified image is a modifita bildo.
- redakti — to edit
- ŝanĝi — to alter
- modifi — to modify
- retuŝi — to retouch
- bildoredaktado — image editing
- bildoredaktilo — image editor
- fotoredaktado — photo editing
- fotoredaktilo — photo editor
- rastrumera redaktilo — raster editor
- vektora redaktilo — vector editor
- bildodosiero — image file
You can find more Esperanto computing terms at Komputeko.