EDIT

    @Test

    public void testSomething(){

       String MCL = "MCL[0-9]{1,3}(\\-[0-9]{1,4}(\\-[0-9]{1,4}(\\-[0-9]{1,3}(\\-[0-9]{1,3})?)?)?)?";

//        String MCL = "a{1,3}";

        String filter = "Acc "+MCL;

       String notes = "Acc: 0x is Hieracium djimilense subsp. neotericum Zahn MCL293-3140-00-630";

       String result;

       if (notes.matches("Acc:.*")){

           if (notes.matches("Acc: .*\\$$") || (notes.matches("Acc: .*"+MCL))){

               result = null;

           }else if (notes.matches("Acc: .*(\\$|"+MCL+")\\s*\\{.*\\}")){

               notes = notes.substring(notes.indexOf("{")+1, notes.length()-1);

               result = notes;

           }else if (notes.matches("Acc: .*(\\$|"+MCL+")\\s*\\[.*\\]")){

               notes = notes.substring(notes.indexOf("[")+1, notes.length()-1);

               result = notes;

           }else{

               logger.warn("Namenote: " + notes);

               result = notes;

           }

       }else if (notes.matches("Syn:.*")){

           if (notes.matches("Syn: .*\\$$") || (notes.matches("Syn: .*"+MCL))){

               result = null;

           }else if (notes.matches("Syn: .*(\\$|"+MCL+")\\s*\\{.*\\}")){

               notes = notes.substring(notes.indexOf("{")+1, notes.length()-1);

               result = notes;

           }else if (notes.matches("Syn: .*(\\$|"+MCL+")\\s*\\[.*\\]")){

               notes = notes.substring(notes.indexOf("[")+1, notes.length()-1);

               result = notes;

           }else{

               logger.warn("Namenote: " + notes);

               result = notes;

           }

       }else{

           result = notes;

       }

       System.out.println(result);

    }