While post-processing your digiscoped images in the "digital darkroom" adds a creative element to your work, various noise reduction software programs will help to speed up the processes. After years of utilizing a technique of painstakingly separating layers and applying blur filters to background areas, I've recently benefited from utilizing such software. While there are a multitude of options out there, I've found Imagenomic's Noiseware 2.5 (freeware) to be one of the fastest and easiest to use.
Click on the above Killdeer image to get an idea of what Noiseware can do for you. To view the final result that I published on my digiscoping website, click here.
Here's another great Noise Reduction package: Noise Ninja
Killdeer image © 2005 Michael Allen McDowell