Read Serial Buffer

int ledPin=13;
int val=0;
char msg= ' ';

void setup(){
  pinMode(ledPin, OUTPUT);
  digitalWrite(ledPin, LOW);
  Serial.begin(9600);
  Serial.flush(); //clean out the serial buffer
  Serial.print("Program Initiated\n");
}

void loop(){
  while(Serial.available()>0){
    msg=Serial.read();

    switch (msg) {
    case 'Y':
      digitalWrite(ledPin, HIGH);
      Serial.print("LED Activated \n");
      break;
    case 'N':
      digitalWrite(ledPin, LOW);
      Serial.print("LED off \n");
      break;
    }
  }
}