This paper studied the development of STEM identity for freshman students in Engineering. An Urban Research University received a 5-year S-STEM award in fall 2018. So far, two cohorts of scholars have received the scholarship as well as academic support, mentoring support, and customized advising from faculty and upper level peers. The objective of this project is to help underrepresented and talented students in engineering to pursue an undergraduate degree. A Multi-Layered Mentoring(MLM) Program was established, and several interviews were conducted with scholarship recipients. The qualitative and qualitative analysis of the student success shows an improvement in GPA of students in the program as compared to the rest of the school. The students not only received financial help through the program based on their unmet needs, they are were placed in an engineering learning community (ELC). The participants in ELC and MLM programs agreed to participate in research studies to assess their success. This NSF funded program also helped freshman students be involved in a hands-on Design Innovations class where they learned design process and human centered design. The students were surveyed on a regular basis to identify their needs and were approached by faculty advisor as well as their mentors to trouble shoot their concerns and help them with both social and academic aspects of their concerns. The first cohort joined the program in AY 2019-2020, as freshmen. This cohort had experienced a full semester of in-person engagement before the COVID-19 hit in the middle of the second semester of their freshman year. We have researched the impact of the pandemic on their academic progress, sense of belonging, and STEM identity. The second cohort joined the program in AY 2020-2021. They have not had the chance to experience the campus life and their perspective of college life is very different than the first cohort. The STEM identity was one of the success indicators for freshman students who entered the university in one of the most difficult and un-usual circumstances under the COVID-19 pandemic.