John Arthur Jones, of Bodffordd, denies 13 counts of recklessly or negligently acting in a manner likely to endanger aircraft or persons in an aircraft.
RAF Valley's commander rejected letters from the 65-year-old.
Mold Crown Court heard he also recorded pilots flying low over Park Cefni.
Giving evidence, Group Captain Peter Cracraft said the letters were "incredible and frankly nonsense".
Asked what he meant, he said pilots had a very structured training programme, and were highly supervised by extremely professional and dedicated instructors.
Everything that occurred in an aircraft was recorded in two independent ways and there were independent observers in the control tower.
"If they were to see any pilots acting in the way Mr Jones alleged, that pilot would not be at RAF Valley for very long," he said.
On Thursday, the commander will be asked to watch video footage compiled by the defendant.
Earlier, a Hawk fighter jet pilot told the jury how he was "lamped" on his first solo night time flight and he had to abort a landing when it happened a second time.
The trial continues.
A man accused of shining bright lights into the cockpits of RAF planes during night flights on Anglesey made some allegations against pilots which were "frankly nonsense", a court heard.