I suppose you can make an ISO file. There is an option in the Tools/Settings to do that.
Probably what you might better want is go into Tools/Settings (IFO Mode Tab) and set File Splitting to "None". Ive never used or tried that, as I have no reason to, particularly as I have a mix of drives/computers some of which involve FAT formatted drives, but also because Ive simply have had problems moving huge files around. Also, not sure what "DvD Shrink" will do with a single file. (I find that it is important to be able to get access to the pieces of the movie for potential editing purposes - getting rid of previews and ads for example.)
Not sure about the current issue that you are experiencing. Dont understand "convert to the HD" means. You should decrypt from CD into a designated folder established on a suitable HDD. After that play the decrypted movie from the folder using a suitable player or copy the folder to some other location that has suitable space or create (ie, write) a decrypted DvD from the folder using a suitable DvD authoring application such as Roxio or NERO. If you are trying to "convert something" then I dont know what that is (although I suppose you could do something like use NERO to create an ISO from a movie folder that was decrypted in VOBs). Choose your poison.