Your arduino sketch is already C code, it just happens to have a set of libraries that hide the hardware from you and allow the code to be used with different hardware with little or no changes.
So I would assume that you want to use a more traditional compiler like Atmel Studio that is based on Visual Studio 2015. This will still let you code the same way as a Sketch if you want, but also will allow you to create programs that will run without the boot loaders etc. There are plenty of examples along with Atmel Studio to give you a head start.
I suggest that you install AVRStudio. This is a full arduino supported environment and makes you the life extremely easy to make this porting. Take in account the following:
.ino "sketches" are as a matter of fact C source files iwth some limitations
You can already add your own C files to a sketch, it is just the case of the Arduino libraries
As a initial startup after the installation of the AVRstudio and the Arduino support plugins you can barely import your original sketches in an AVRStudio project then move for the conversion (with a lot of documentation and helpful contextual hints).
There is a very high compatibility level between the AVRStudio and the java arduino IDE
The only limitation is that after a sketch has been ported inside a AVRStudio project you should have a backup because you can no longer open the .ino sketch with the Arduino IDE (but this is not your need).
For any specific detail, just ask here.
Note: clem57 is right with his suggestion and hte documentation link is a great compendium. The use of AVRStudio instead gives you the option to compile the code and upload to the Arduino board like before.
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