Unlike genomic DNA, cfDNA has specific fragmentation patterns. The ambiguous definition of "fragment length" by various alignment software is raising concerns: see page 9 footnote in SAM file format spec: https://samtools.github.io/hts-specs/SAMv1.pdfcell-free DNA data fragmentomic analysis requires single-molecule level resolution, emphasising the importance of accurate/unbiased feature extraction. The traditional tools built for solid tissue sequencing do not consider the specific properties of cfDNA sequencing data (e.g., cfDNAs are naturally fragmented with a modal fragment size of 167bp, and di-/tri-nucleotide peaks in the length distributions). Researchers might inadvertently extract the features using a sub-optimised method. cfDNAPro is designed to resolve this issue and standardize the cfDNA fragmentomic analysis, complying with the existing building blocks in the bioconductor R ecosystem. We wish cfDNAPro to provide a catalyst for further improvements in the implementation and development of cfDNA biomarkers and multi-modal AI for various health conditions.