Hi there,
I think you need to stop for a moment and ask yourself what you're coding. I dont mean this harshly, but Im sure that anyone new to coding is going to go steaght in and make something work. It is satisfying, but not pretty!
You have used the main method 3 times, did you really mean this? Remember the main method is your entry point to an application. Once you're up and running, why start more applications? This may be your problem (although I've not tested it).
Try to describe your application first. Name some objects that you think you might need, what methods they might have and what those methods will do.
For example this sounds like some kind of text filter application. So your class with the main method could be FileFilterApp. You could maybe have a TokenList (a list of all the tokens to remove), that would suggest a Token. These might be used by a FileFilter.
So, lets expand on that a bit:
A Token could have some methods like:
public Token(String token) //constructor
public String getToken() //get the Token value
A TokenList could have:
public TokenList() //create an empty list
public addToken(Token token) //add a token to the list
public removeToken(Token token) //remove a token forn the list
public iterator() //get the token list iterator for walking the list
A FileFilter could have
public TextFilter(TokenList list) // create a filter using this token list
public File filter(File file) // filter file based on list
public String filter(File file) // filter file based on list
public StringBuffer filter(File file) // filter file based on list
Finally, your FileFilterApp might look something like:
This is intended only as a starting point, so come back if you need more help.