1. In an exhaustive manner
   "we searched the files thoroughly"
   - exhaustively 
2. Completely and absolutely ('good' is sometimes used informally for 'thoroughly')
   - soundly, good

See also: thorough

• second thought
• second to none
• second trimester
• Second Vatican Council
• second wind
• Second World War
• second-degree burn
• second-guess
• second-hand speech
• second-hand store
• second-in-command
• second-place finish
• second-rate
• second-rater
• second-sighted
• second-stringer
• second-year
• secondarily
• secondary
• secondary amenorrhea
• secondary cell
• secondary censorship
• secondary coil
• secondary dentition
• secondary diagonal