No magic wand... The real problem likely lies in the way you go from canvas to digital image...
For a photo, if you light the canvas from the side there will be shadows and the texture will be very visible. If you light the canvas from the camera (built-in flash or cobra flash on the camera...) or with two opposing light sources (that cancel each other's shadows) there won't be much shadowing and the texture won't be too visible.
For a scan, the scanner's light is a bit on the side from the sensor so you get some shadows. You cannot change this but it usually easy to scan after rotating the scanned paint 180° in the scanner. In the second scan the shadows will be on the opposite side of the texture. You load both pictures in Gimp, align them, and put the top layer in Lighten only mode to remove the shadows.
Put you can always post an extract of what you have so far so we can give a more focused advice.
For a photo, if you light the canvas from the side there will be shadows and the texture will be very visible. If you light the canvas from the camera (built-in flash or cobra flash on the camera...) or with two opposing light sources (that cancel each other's shadows) there won't be much shadowing and the texture won't be too visible.
For a scan, the scanner's light is a bit on the side from the sensor so you get some shadows. You cannot change this but it usually easy to scan after rotating the scanned paint 180° in the scanner. In the second scan the shadows will be on the opposite side of the texture. You load both pictures in Gimp, align them, and put the top layer in Lighten only mode to remove the shadows.
Put you can always post an extract of what you have so far so we can give a more focused advice.