You could try this:
char value = 0;
void setup()
{
Serial.begin(9600);
}
boolean ready = false;
void loop()
{
if (!ready){
//first 3 seconds
if( millis() > 3000)
{
ready = true; //3 seconds has passed.
}
else if(Serial.available())
{
Serial.read(); //clear any characters arriving early.
}
}
else {
//After 3 seconds:
if(Serial.available())
{
value = Serial.read();
}
}
}