Dan,

In that case, using a backup/imaging application such as Acronis or Ghost will do what you want, though you will have to go through the process of selecting only what folders and files you want to make a backup/image of.

Having said that, once you've set it up, you will be able to take periodic backups as and when you want and it will only grab the files and folders that you want whilst retaining their architecture.

After doing some research, Acronis looks like a good bit of software and it's feature list suggests you can do exactly what you want to do with it. There are cheaper alternatives out there, but if you can afford it then it will be money well spent in my opinion - experienced users can get away with doing it themselves, those looking for an easy way to back up only portions of their hard drive and have the ability to restore are much better catered by software such as this.

Give it a go and if you have any problems don't hesitate to get in touch. Best of luck.

John