I need to deploy my custom modules from 1.9.X to 2.0.X,
Is there any way to deploy, or we will start from scratch.?
You can use of Code Migration Toolkit.
The Magento Code Migration Toolkit provides scripts that ease the process of converting custom Magento 1.x code to Magento 2 by handling some of the most time-consuming conversion tasks. The toolkit is intended for Magento developers with reasonable expertise in both Magento 1.x and Magento 2.
The toolkit covers migration of the following aspects of the Magento code:
Module directory structure
Layout XML files
Config XML files
Migration of Magento modules is the focus of the toolkit. Magento themes are out of scope of the toolkit at the moment.
The toolkit can significantly reduce the work involved in the code migration. However, after running the toolkit one will need to manually edit some of the generated files.
Magento 1.x modules are not compatible with Magento 2.x
You will have to port your M1 modules to M2 manually.
You need to adapt your Magento 1 code with Magento 2.
If you need to migrate old Magento 1 data to Magento 2 you can based on the Magento 2 data migration tools.
And set up your custom schema mapping.
More information here : http://devdocs.magento.com/guides/v2.0/migration/migration-tool.html