How to create a 38 Khz pulse with arduino using timer or PWM?

Will the above code interfere with these?

No.

since you code uses interrupt which interrupt I can't utilize in further coding?

As the code uses pin 3 you can't use that pin as an interrupt, but if that is a problem just change it to use pin 11 instead of pin 3.

Also I understand pin 3 and pin 11 cannot be use for any other purpose

If that is what you understand then you are wrong.