1)Is it possible to organise imports on all the java files under a single project rather going for individual file at a single touch?
This is an Eclipse functionality and yes, just right click on the folder and do Source > Organize Imports, it will recursively apply to all files.
2) Is it possible to eliminate the unused instances and methods in a java file thru MyEclipse tool?
No, this would be supported by another plugin if it existed.