Chiral enantiomers have different pharmacological and pharmacokinetic characteristics. It is important to strictly detect chiral component for avoiding being harmful to the human body due to side effects. Terahertz (THz) trace fingerprint detection is essential because the molecular vibrations of various biological substances such as chiral enantiomers are located in THz range. Recent reported enhanced trace fingerprint technologies have some drawbacks. For instance, multiplexing technology suffered from narrow operation range and limitation by frequency resolution of commercial THz time domain spectroscopy; Absorption induced transparency (AIT) identification for narrowband molecular oscillations suffered from random resonance frequency drift due to fabrication error. In this paper, we proposed frequency-selective fingerprint sensor (FSFS), which can experimentally achieve enhanced trace fingerprint detection by both broadband multiplexing technology and robust AIT identification. Such FSFS is based on polarization independent reconfiguration metasurfaces array. Broadband absorption lines of trace-amount chiral carnitine were boosted with absorption enhancement factors of about 7.3 times based on frequency-selective multiplexing at 0.95–2.0 THz. Enhanced trace narrowband α-lactose fingerprint sensing can be observed at several array structures with absorption enhancement factors of about 7 times based on AIT, exhibiting good robustness. The flexibility and versatility of proposed FSFS has potential applications for boosting trace chiral enantiomer detection as well as diversity of molecular fingerprints identification by both multiplexing and AIT.