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This question already has an answer here:

Using Gimp, I want to make a small part of an image transparent. However, when I use colour to alpha, it turns the whole image partially transparent by removing the colour from all pixels.

Is there a way to stop this?

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marked as duplicate by Ilmari Karonen, Scott, Yisela Apr 7 '13 at 23:55

This question was marked as an exact duplicate of an existing question.

Welcome to GD.SE! If you would describe expected outcome a bit more or give an example image I might be able to give a more specific answer. :) – Cust0dian Apr 6 '13 at 10:43
Short version of the answer Cust0dian linked to: select the part you want to make (semi)transparent, then use Color to Alpha. – Ilmari Karonen Apr 6 '13 at 11:07

I think what you are looking for is Layer mask:

A Layer Mask is linked to a layer and hides part of the layer from the picture. What is painted black on the adjustment layer will not be visible in the final picture. What is grey will be more or less transparent depending on the shade of grey. As the layer mask can be both edited and moved around independently of both the background layer and the layer it applies to, it gives the user the ability to test a lot of different combinations of overlay.

Or, if you want to get more technical, you can read more about Layer masks on GIMP docs.

There are many videos about the actual process of creating Layer mask in GIMP.

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