Hi @Nico1978
Welcome to the forum.
the ‘disturbing’ structures are produced by the edge filter. You will never get complete rid of them.
Here are some ideas, packed in ImageJ macro code.
- You can smooth your image before applying the edge filter, like this:
run("8-bit");
run("Gaussian Blur...");
run("Find Edges");

or you can
- threshold the edge filtered image, fill the holes in this thresholded image and use it as a mask:
rename("orig");
run("8-bit");
run("Find Edges");
run("Duplicate...", "title=dub");
setAutoThreshold("Default dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Close-");
run("Dilate");
run("Dilate");
run("Erode");
run("Erode");
run("Divide...", "value=255");
imageCalculator("Multiply create", "orig","dub");
selectWindow("Result of orig");
selectWindow("dub");
close();

Maybe this will help you to get started.