Unfortunately, layers are not implemented yet. They will be in the final product.
For now, you can only send an object/shape forward and backward in the general hierarchy using the CMD + [ and CMD + ] shortcuts.
Will the layers in final version be compatible with After Effects?
I am a really big fan of XD already and have started using it in aspects of larger scale projects, however sometimes we will need to show a contextual video or specific interactions in a prototype design. Using layers from PSD, AI it is super super simple to get this done, so I am keen to know whether XD layers will also play nice with AE?
This is something we're considering. You can upvote the idea here and get more information about our progress: Export to After Effects to add animation – Adobe XD Feedback : Feature Requests & Bugs
Awesome, thanks Elaine!