The 21-year-old disappeared after a night out with friends at the Welly nightclub in Beverley Road in the early hours of Feburary 1.
Following extensive searches, her body was recovered from the Humber Estuary just over six weeks later on Wednesday, March 20
Pawel Relowicz was charged with Libby's murder and rape earlier this month.
Relowicz, 25, appeared at Hull Magistrates Court via video link from HMP Wakefield on Wednesday afternoon.
He spoke only to confirm his name, age and nationality.
The charges he faces were read out in court by the legal advisor.
The second charge of rape was alleged to have taken place between January 31 and February 1.
Prosecuting Kate Fairburn said: "These are matters that can only be dealt with at the Crown Court.
"They are indictable only matters and I ask that the case be sent to Hull Crown Court."
Relowicz, formerly of Raglan Street, will appear at Hull Crown Court tomorrow at 10am.
No application for bail was made and Relowicz was remanded into custody.