Officials say the pilot saw a green light being flashed at him while flying in the area of Cambridge and Channing around 3:00 am.
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The 25-year-old suspect was standing on the roof of his home. Authorities say he aimed the laser at the aircraft several times.
CHP officers and Fresno police went to the house where they found the suspect.
"Any consistent laser pointing can cause damage, and in California, it is an assault charge for shining a laser pointer at any aircraft," said CHP Sgt. John Tyler.
The suspect is being charged with both state and federal crimes.
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Officers were speaking with him to determine why he did it.
The CHP pilot was not injured and safely landed the aircraft, officials said.