Noticed a few people have been having this problem (as I did) of achieving a clean install with Windows 8 on a SSD, on a pre-installed Windows 8 system. So here is how I managed to performed this operation.
The main two problems seem to be: 1) You don't get an installation disk these days. 2) You can only download the ISO file for the Windows 8 Pro version. Which is how you would of ordinarily of done a fresh install if you didn't have an installation disc.
How I got around this is by simply creating system recovery media in the form of a USB Flash drive. In my case it was HP Recovery Media but in your case it will probably be whatever manufacturer you are with. It will only let me create this media once. I used a 32GB USB Flash drive, I tried 16GB one but it wasn't big enough.
Once you have done this install your SDD into your system, insert the USB recovery media and switch your system on. It should now guide you through the process of installing Windows 8 on your SSD, depending on your manufactures recovery media. It will first copy the recovery partition to your SSD. Windows 8 should detect that it is installing onto a SSD and setup accordingly with proper alignment and automatically adjusting the likes of disk defrag.
Although this is not strictly a freh install of Windows 8, as in it will include some manufacturers bloatware it is the closest thing I could find without an installation disk or ISO file.
Your SSD should now be correctly installed. It was in my case but I ran into a slight problem.
I had taken out the DVD drive and installed my HDD in itís place using a optical bay caddy. When I fitted it my laptop started to boot from the HDD rather than the SSD. It had also decided to move my SSD from drive letter C: to drive letter E:. My HDD was C: and recovery partition on that drive was D:. I tried changing this in disk management and in my computer but to no avail. Ordinarily you would be able to just change the booting order in the BIOS but my Laptop would not allow this. I finally attempted to boot my laptop from the SSD then once I was in Windows insert the HDD caddy with the laptop still on. It did not recognise the HDD so I decided to restart the system. When I restarted the system it booted from the SSD. Once in Windows I checked my computer, it had moved my SSD back over to letter C: and my HDD is now D: (and the recovery partition of this drive now E:. It has booted from the SSD ever since and has been running smoothly.
I decided to delete the main partition on my HDD to free up extra space and one hundred percent stop the computer from getting confused of which drive to boot from. You do this by formatting the partition. This is achieved by opening my computer, right clicking the partition you wish to format and clicking format. I decided to not delete the recovery partition off my HDD drive though.
Anyway, hope this helps anyone trying to perform this operation.