The new charges also significantly expand the timeline in the Gilgo Beach case, with the first murder Heuermann is accused of committing now taking place in 1993.
Prosecutors also revealed disturbing "planning" documents that they allege the suspect used in his killings and disposal of the victims.
The architect and father allegedly "meticulously planned and executed six separate murders," Suffolk County District Attorney Raymond Tierney said at a news conference Thursday.
Heuermann appeared before a judge on Long Island to face charges in the killings of Jessica Taylor and Sandra Costilla, two young women who were long suspected of being the victims of men preying on sex workers.
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Taylor disappeared in 2003. Costilla was killed in 1993.
Costilla's murder was long thought to be the work of another person. Her remains were found in North Sea, in the town of Southampton.
In a court filing, prosecutors said they were able to use new forensic testing methods to match hairs found on or near the vicinity of both victims to a DNA profile that is a likely match to Heuermann. Additionally, prosecutors say they recovered a "planning document" on a hard drive in his basement used to "methodically blueprint" his killings.
The all-caps document features a series of checklists with tasks to complete before, during and after the killings, as well as practical lessons for "next time." Among the dozens of entries written are reminders to clean the bodies and destroy evidence, to "get sleep before hunt" and to "have story set."
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One section, titled "things to remember," appears to highlight lessons from previous killings, prosecutors said, such as using heavier rope and limiting noise in order to maximize "play time." A "body prep" checklist includes, among other items, a note to "remove head and hands."
Prosecutors believe that entry may connect Heuermann to yet another victim, Valerie Mack, whose partial skeletal remains were discovered near the body of Taylor after her disappearance in 2000.
Heuermann has not been charged in the death of Mack. But asked during a news conference after Thursday's hearing if he was a suspect, District Attorney Ray Tierney replied, "That's fair to say."
He added that investigators are still working the case, noting that the "method of the crime scene" in Mack's killing was consistent with those of the other victims.
Heuermann pleaded not guilty to killing Taylor and Costilla during the hearing and was ordered held without bail.
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Court documents said that Taylor was decapitated and her arms had been severed from her torso.
Investigators believe the mutilations, "were acts perpetrated by Rex A. Heuermann to inhibit the identification of the victim via facial recognition, fingerprints and/or tattoo identification," according to a newly unsealed court document.
Taylor's skull, hands, and forearm were discovered along Ocean Parkway, just east of Gilgo Beach, near the spot where the remains of other victims were discovered.
Investigators linked Heuermann to her death in part through DNA from a male human hair recovered from her body, specifically from a surgical drape that had been underneath the victim, according to the court document.
Investigators also said phone records established that Heuermann's wife and children were out of town at the time Jessica Taylor was killed.
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"Accordingly, the murders of all four charged victims, and now the murder of Ms. Taylor, occurred at times when Defendant Heuermann's wife and children were located out of state, which would have allowed Defendant Heuermann unfettered time to execute his plans for Ms. Taylor, which included the decapitation, dismemberment, and transportation of her remains, without any fear that his family would uncover or learn of his involvement in these crimes," the court document said.
The charges involving Costilla, who was killed 30 years ago, indicate that prosecutors believe Heuermann was killing victims for much longer longer than previously thought. Unlike the other victims, Costilla's remains were not among those discovered at Gilgo Beach, but were found in a wooded area in Southampton, Long Island.
Since late 2010, police have been investigating the deaths of at least 10 people - mostly female sex workers - whose remains were discovered along an isolated highway not far from Gilgo Beach on Long Island's south shore.
Tierney said the planning document was recovered in March of this year, providing the impetus for the recent searches at the suspect's home and in Manorville.
Prosecutors also said they found a book in Heuermann's possession by the retired FBI agent John Douglas, "The Cases That Haunt Us." They say the planning document referenced specific pages in another work by Douglas, "Mind Hunter," that allude to the personality types of serial killers and profiles of those who use mutilation and sexual violence.
Investigators have also used Heuermann's significant collection of violent, bondage, and torture pornography, currently dating back to 1994.
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"The pornographic images accessed by Heuermann," court records said, "notably and largely coincide with how the remains of Sandra Costilla, Jessica Taylor and Valerie Mack were discovered."
There has been a sweeping expansion of the investigation into Heuermann, a former New York City architect, following his arrest last summer.
At least 11 sets of human remains have been found in Long Island's Suffolk County, including the four women Heuermann is accused of killing: Megan Waterman, Melissa Barthelemy, Amber Costello, and Maureen Brainard-Barnes.
Their remains were found near Gilgo Beach along Ocean Parkway.
Heuermann has pleaded not guilty to all murder charges.
He was remanded without bail. His next court date is July 30.
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Some information from ABC News and the Associated Press