Specifically, her research has focused on the violence which occurred during the Guatemalan Civil War and rebuilding the structures to support the country's democracy.
When the Peace Accords were accepted in 1996, Hernández worked with the Historical Clarification Commission and then with the Myrna Mack Foundation, hoping to assist families in gaining information to prosecute human rights violations which occurred during the war.
Hernández has written numerous reports analyzing the war and the processes necessary re-establish systems which offer both transparency and provide for state security within a democratic framework.
[2][9] As an expert witness in the case to investigate and prosecute those who murdered Mack, a protection order was issued because of threats to her safety and remained in place from 2003 to 2009.
[5][12] Through the organization, she carries out research into atrocities committed during the war, seeks resolution for victims of state violence, and works to improve the processes of democracy and reform in Guatemala.
[2][5] In 2003, Grupo de Apoyo Mutuo (GAM, Mutual Support Group), an association dedicated to helping those with disappeared family members,[13] and SEDEM worked with the Procuraduría de los Derechos Humanos (PDH, Human Rights Ombudsman's Office) to assist in processing the archives of the Estado Mayor Presidencial (EMP, Presidential General Staff), when the EMP was dissolved as per requirements of the Peace Accords.
[14] They were joined in 2004, by the Centro Para la Acción Legal en Derechos Humanos (CALDH, Center for Human Rights Legal Action), Hijos e Hijas por la Identidad y la Justicia y Contra el Olvido y el Silencio (HIJOS, Sons and Daughters for Identity and Justice and Against Forgetting and Silence) and the Oficina de Derechos Humanos del Arzobispado de Guatemala (ODHAG, Human Rights Office of the Archbishop of Guatemala) to digitize the records and prevent their destruction.
[15] Because of the urgency of the work and the lack of international funding, the context of the images on the more than seven hundred discs were lost, meaning that they were not recorded in sequence or with regard to their relationship to other documents.
[19] Gaining financial support from international archivists, the groups were able to process the archives for scientific preservation while balancing the need to address the human rights investigations in a timely manner.
[22][12] Since that time, Hernández has organized seminars and workshops on both the national and international level to provide training on security reform and implementation of democratic controls.
In April 2012, she was also included in an accusation filed by a family member of a military officer against over one hundred people, who supposedly committed disappearances, and participated in genocide and terrorism against society between 1960 and 1985.
The Protection Unit for Human Rights Defenders of Guatemala discovered that the case had initially been filed giving an incorrect address for Hernández's notification and a first hearing had occurred in June without her knowledge.