Can LE search the entire vehicle even if the K9 only alerts/indicates on a specific area of the vehicle?

While this question has not been addressed on point, the answer is most probably yes. This is a two-step analysis; 1) probable cause and 2) what can be searched. For the first step, the U.S. Supreme Court has recognized that a well-trained K9’s alert provides probable cause to search. “A detection dog recognizes an odor, not a drug, and should alert whenever the scent is present, even if the substance is gone.” Florida v. Harris (2013) 568 U.S. 237, 248. For the second step, once probable cause is established that controlled substances are somewhere in the vehicle, a search of the entire vehicle, including the truck and engine compartment, is justified. People v. Hunter (2005) 133 Cal.App.4th 371; People v. Dey (2000) 84 Cal.App.4th 1318; finding that United States v. Ross (1982) 456 U.S. 798 has, in effect, overruled prior cases to the contrary. E.g.; see Wimberly v. Superior Court (1976) 16 Cal. 3d 557; People v. Gregg (1974) 43 Cal. App. 3d 137.) If probable cause justifies the search of a lawfully stopped vehicle, it justifies the search of every part of the vehicle and its contents that may conceal the object of the search. United States v. Ross (1982) 456 U.S. 798, 823. In People v. Chavers (1983) 33 Cal.3d 462, the California Supreme Court ruled that a search of a vehicle which included a search of the glove box and a shaving kit within the glove box was constitutional because LE had reasonable cause to believe evidence of a recently committed crime were present (armed robbery).

Finally, courts have recognized that K9s alert to the smell of controlled substances, not the actual drug itself. Therefore, there are understandable situations where a K9 will alert but contraband is found in another location in the vehicle. This is because of the way scent can travel, how scent can be left behind on door handles or trunk latch, and that controlled substances’ scent can be left behind even when the controlled substances have been removed.