Investigators had "returned to an area of interest near the Leon River, Bell County, Texas, to conduct further investigative work" and discovered partial human remains, the Army CID said.
Authorities said the identity of the remains has not been confirmed.
The remains were found in a shallow grave and search operations have been suspended, pending identification, Tim Miller, director and founder of Texas EquuSearch, told CNN.
Miller said the discovery was made approximately 26 miles from the site where authorities in early June found the remains of Gregory Wedel-Morales, a soldier who went missing last year while driving his car in Killeen.
While it is unclear if there is a connection between Guillén and the remains, an attorney representing the soldier's family said his clients were heartbroken and continue to ask for the truth about the soldier's disappearance.
"Our hearts are broken. We feel pain, frustration and devastation. This should not have happened. We demand an investigation by Congress. We demand the truth," attorney Natalie Khawam told CNN in a statement. "If this can happen to Vanessa, it can happen to any of our sisters, daughters and mothers."
Before Guillén disappeared, he had told his family that he was being sexually harassed by one of his sergeants at Fort Hood, according to the website his family created to promote the search. She did not identify the sergeant.
Guillén, a private first class, was last seen wearing a black T-shirt and purple fitness pants, according to the Army CID. His car keys, room key, ID card, and wallet were later found in the armory room where he worked the same day.
Guillén describes himself as 5 foot 2 inches, 126 pounds with black hair and brown eyes, according to the CID statement from the military.