I am a total newbie of using gimp. I tried to combine three plots into a figure, but got the first plot having white background. Is there way to remove the white background and then merge all the layers into one, and then fill the background with white? Thanks,

First an explanation as to why you will run into problems trying to adjust your 3 layers.

The background layer has both alpha (transparency) and pixels locked. You might have done this to fix the layer location. That is not their purpose. Easy to click on the icons and unlock. see attachment

Then you could apply Colors -> Color-to-Alpha to remove the white and put a new white layer at the very bottom of the stack.

However the quickest way.

With the top layer active Layer -> New Layer from visible to combine the 3 layers.

With the background colour white. Layer -> Transparency -> Remove Alpha Channel see attachment.

rich: www.gimp-forum.net

Thanks for the clear explanation. I have followed both your ways to fix the issue. Actually it seems skipping creating a new layer from visible also works, just unlock the lowest layer which I have no idea when locked, and then merge till the last, then remove the alpha channel, that seems to give the same result.

Towards your second way, I have the following questions would be really appreciated if you could help,

(1) wouldn't filling in the top layer with color overshadow the layers beneath it?
(2) after merging layers into one, can I still operate on previous layers? most likely not, if so then what's the purpose to create a new layer from visible? I followed this concern to come up with my own mentioned above.
(3) is removing alpha channel equivalent to filling the background with white?

BTW, how do I see whether the pixel and alpha channel are unlocked? I clicked on it, but no signs showing that they are unlocked although indeed then I can erase and make modifications.

The second way

(1) (2) Yes, Losing the alpha-channel on the new-from-visible does hide the layers under it. The main reason for using it is non-destructive. The original layers will be there in case later editing is required. Remember to save your work in xcf format. All layers, masks, guides, text layers .... are saved.

The new-from-visible layer can be hidden by toggling layer visibility - the little eye icon.

(3) Removing the alpha channel will replace transparent pixels with the background colour, not necessarily white.

Lock pixels/alpha icons state can be a little difficult to see when using Windows. That screenshot I put up is in linux. Look for a border after clicking the icon - see attachment