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They believed her body had been buried in a park or reserve near her North Shore home, or dumped in a waterway. They were confident they would find her.
And last night they said that they had - in a waterway in a reserve near her home in Torbay.
Detective Inspector Bruce Scott said the discovery of Ms Chen's body was a breakthrough, but an arrest was not expected immediately. "There is plenty of work still to be done."
He would not be drawn on suspects or a motive for the 44-year-old's murder.
Ms Chen was last seen on November 5, 2012, after leaving the accountancy firm she worked at. She drove to home, parked her car and went inside.
Her partner, Yun Liu, known as Jack, reported her missing at 9.30 that night.
He said she had left the house to go walking at 5.30 and had not returned.
He usually walked with her, but told police he had injured his leg so had stayed home. He has remained in contact with detectives and is understood to have been co-operative.
Initial searches of green areas near Ms Chen's home yielded no clues. Police appealed for sightings of her and of a white 2002 Nissan Pulsar station wagon that they said was "crucial" to the investigation.
Soon after Ms Chen disappeared, Mr Scott told the Herald that the investigation team believed she was killed at or near her property.
That belief was based on the fact that no trace of Ms Chen was found, and no sightings were reported when she disappeared despite the fact it was a busy Guy Fawkes night.
On Monday last week, police got the break they were hoping for when a contractor mowing the lawns at the Totaravale Reserve found a ribcage and skull in a drain.
Most of the rest of Ms Chen's remains were found nearby.
Mr Scott said: "The area that Cissy's body has been found in was well known to both Cissy and her partner. They lived nearby and used to walk regularly around the neighbourhood.
"We're now working through the information gathered from last week's scene examination, and an area canvass of residents in the neighbourhood is also underway."
The site where Ms Chen's remains were found will be blessed by a local kaumatua this morning.
Cissy Chen's remains were identified using forensic dentistry, the Herald has learned.
It is understood that most of Ms Chen's skeleton was recovered from a drain at Totaravale Reserve last week, including her skull and teeth. When a body is found, police either use DNA profiling or forensic dentistry to confirm who the remains belong to.
If the former is used, forensic scientists work to confirm the identification of remains by their respective DNA profiles.
If DNA samples cannot be obtained from remains because of their age or condition, a forensic dentist is used to establish the identity.
A forensic dentist will analyse the teeth against dental records to confirm identity. If no dental records are held, the job becomes much harder and a profile is created of the deceased, including information on their race, age and gender, based on their specific dental structure.
Formal identification of a body can take weeks depending on what is found and what medical records are available to match against the remains.
Can you help?
If you have information about the murder of Cissy Chen, or you lived in the Totaravale Reserve area in November 2012 but have since moved, police want to speak to you. Contact the Operation Waiau team on 0800-024-779. Information can also be provided anonymously through Crimestoppers on 0800-555-111.