Jeff Morales, chief executive of the rail authority, said the agency takes farmers' concerns seriously and wants to address them.
With the court decision out of the way, "we can begin interacting with property owners much more directly and start working with them to address their particular concerns," he said outside court.
The rail authority has already surveyed more than 300 parcels of land along the proposed route since Gov. Jerry Brown signed legislation giving his approval in July.
Lawmakers approved the first phase of the planned 800-mile line this summer, allowing the state to begin selling $2.6 billion in bonds for construction of the first 130-mile stretch of the bullet train in the Central Valley. That approval also allowed the state to tap $3.2 billion from the federal government.
The money is contingent upon completing the first phase of the project by 2017, requiring what officials say is an unprecedented construction pace.
Voters approved issuing $10 billion in bonds for the project in 2008, but public support for the plan has dwindled in recent years as the project's expected costs have soared. The most recent estimate is at least $68 billion for the completed project linking Northern and Southern California.
In one of their court filings, opponents said rail officials are spending furiously because they hope "to become so financially committed to the currently conceived section alignment that it will be unthinkable to later choose another course."