Refreshing Your Media lasts for a really long time

Mine has 8gb and still almost empty (no more than 1 gb occupied). I was afraid that everytime I copy a single file, the whole memory must be checked to organize the content. Is it not possible to create any kind of log file or something like an index, to check quickly only the differences and not the whole stuff?

I am really scared about copy a lot of files, besides I have to copy and delete frequently.