I made a close button for a gui. Now how would i make the gui fade out?

I highly recommend you use a for loop instead as it is much shorter and looks much cleaner in your code.

button = script.Parent.Parent.Parent
window = button.Parent.Parent.Parent

function onClicked()
    for i = 1, 0, -.05 do
        window.BackgroundTransparency = i
        wait()
    end
    window:Destroy()
end

script.Parent.MouseButton1Click:connect(onClicked)

If your window is an image, use ImageTransparency as well.

button = script.Parent.Parent.Parent
window = button.Parent.Parent.Parent

function onClicked()
    for i = 1, 0, -.05 do
        window.BackgroundTransparency = i
        window.ImageTransparency = i
        wait()
    end
    window:Destroy()
end

script.Parent.MouseButton1Click:connect(onClicked)

You should always ensure that you use :Destroy() instead of :remove() as remove is deprecated and doesn't completely "remove" objects. If there are children to the window that also fade away, you will also need to refer to those in the script. I hope this helped!