You can also use SeqKit to filter FASTA sequences by length. The -M option prints sequences shorter than the maximum length.

seqkit seq -M 101 -o output.fa input.fa

Hi! I believe this command would do what you are looking for.

awk 'BEGIN{RS=">"}NR>1{sub("\n","\t"); gsub("\n",""); print RS$0}'  test.fa | tail -n+1 | awk -F"\t" '{split($1,h,"len:");split(h[2],l," "); if (l[1]<=100){print}}'  | awk -F'\t' '{print $1"\n"$2}'

This "one-liner" does different things:

1) convert fasta into tab format with:

awk 'BEGIN{RS=">"}NR>1{sub("\n","\t"); gsub("\n",""); print RS$0}'  test.fa 

1.5) Remove the unwanted first blank line with:

tail -n+1

2) Filter based on "len:" field in the header with:

awk -F"\t" '{split($1,h,"len:");split(h[2],l," "); if (l[1]<=100){print}}'

3) Go back from tab to fasta format with:

awk -F'\t' '{print $1"\n"$2}'