Three-year-old William was last seen wearing a Spider-Man suit outside his foster grandmother's Benaroon Drive home on September 19, 2014.
Forensic experts have been helping with the search, including hydrologist Jon Olley and forensic archaeologist Tony Lowe.
Some cloth pieces and other items were found during the thorough search.
A car belonging to William's late foster grandmother was also seized.
Police said on Tuesday that forensic examinations continued on seized items and a significant quantity of soil taken from the search site.
New evidence is expected to be put during a coronial inquest.
William has never been found despite years of detective work, the identification of hundreds of people of interest and a $1m reward for information.
Meanwhile, a rake signed by the search team has been erected at the site, which is less than 1km from where the young boy was last seen.
"We will never give up," a message on the handle read.