2305195303310_ABC_A08_1378408840043.hl7

2305195303310_ABC_A08_1378408840043.hl7
Q37984932T467566261_DEF_R03_1378825633215.hl7
37982442T467537201_DEF_R03_1378823455384.hl7
37982442T467537201_MNO_R03_1378823455384.hl7
2305195303310_ABC_A08_1378408840053.hl7
Q37984932T467566261_DEF_R03_1378825633215.hl7
37982442T467537201_MNO_R03_1378823455384.hl7

ABC 3
DEF 3
MNO 2

for i in *_*_*; do echo "$i"; done

cut -d '_' -f 2

$ for i in *_*_*; do echo "$i" | cut -d '_' -f 2 ; done |
   grep . | sort | uniq -c

  3 ABC
  2 DEF
  1 MNO

$ for i in *_*_*; do echo "$i" | cut -d '_' -f 2 ; done |
   grep . | sort | uniq -c | awk '{print $2,$1}'

ABC 3
DEF 2
MNO 1

ls | cut -d_ -f2 | sort | uniq -c