Shell Programming and Scripting

 
sed 's/000000000000000//g' filename > newfilename
 
or
#backup the original file
cp filename newfilename
 
#replace the contents in the original file
sed -i 's/000000000000000//g' filename

sed 's,000000000*,,g;s,+,,g' <input_file>

$ cat input_file
01,011600033,011600033,110516,0801,3,90,,2/
02,011600033,011103093,1,110317,0801,,2/
03,000000000000000000,,056,+00000000000,,,703,+00000000000,

$ sed 's,000000000*,,g;s,+,,g' input_file
01,011600033,011600033,110516,0801,3,90,,2/
02,011600033,011103093,1,110317,0801,,2/
03,,,056,,,,703,,

$

01,011600033,011600033,110516,0801,3,90,,2/
02,011600033,011103093,1,110317,0801,,2/
03,000000000000000000,,056,+00000000000,,,703,+00000000000,,

,904,+00000000000,,/
49,+00000000000000000,00002/
03,004000100015860001,,056,+00029000000,,,703,+00150000000,,

,904,+00000054375,,/
49,+00000000179054375,00002/
03,004000102597629002,,056,+00098668140,,,703,+00100000000,,

,904,+00000197336,,/
49,+00000000198865476,00002/
03,004000104694860002,,056,+00201098996,,,703,+00244527405,,
,904,+00000285805,,/

sed 's/,904,/,905,/g' <input_file>