In most situations, creating modified world generation is easy WITH plugins or mods. However, if you want to have a completely vanilla server with a modified world here is how you do it:
1. Open up your minecraft launcher and start the game. (*Note that this will only work in later versions of the game.). From there, navigate into your singleplayer menu and click "Create New World", followed by "More World Options...".
2. Click "World Type:" until you see "Customized". Once you've found it, click "Customize". This is where you will modify the worlds generation settings. This is completely up to you and beyond our assistance. For more information on customizing the world, please consult the wiki: http://minecraft.gamepedia.com/Customized
3. Once you've customized your world, you can simply upload it using a third party FTP program, such as FileZilla. For assistance on this, we encourage you to follow our guide: https://www.beastnode.com/portal/knowledgebase/75/How-to-Upload-a-Custom-World.html
4. After you've uploaded the world and set it to load on your control panel (more information in the link from Step 3.), you're all set to go!
Enjoy your customized world!