It'd be easier if your native code exposed an interface that let you feed it a stream of bytes, or even a filename instead.
Since the FILE structure is opaque, you don't actually have to map it in JNA, you can generally get by using a Pointer, e.g.
Pointer fopen(String filename, String mode);
void fclose(Pointer fp);
If you want to get fancy and type-safe, you could do:
class FILE extends PointerType { }
FILE fopen(String filename, String mode);
void fclose(FILE fp);
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