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@echo off
setlocal EnableDelayedExpansion

set "startTime=%time: =0%"

set /P "=Any process here..."

set "endTime=%time: =0%"



rem Get elapsed time:
set "end=!endTime:%time:~8,1%=%%100)*100+1!"  &  set "start=!startTime:%time:~8,1%=%%100)*100+1!"
set /A "elap=((((10!end:%time:~2,1%=%%100)*60+1!%%100)-((((10!start:%time:~2,1%=%%100)*60+1!%%100)"

rem Convert elapsed time to HH:MM:SS:CC format:
set /A "cc=elap%%100+100,elap/=100,ss=elap%%60+100,elap/=60,mm=elap%%60+100,hh=elap/60+100"

echo Start:    %startTime%
echo End:      %endTime%
echo Elapsed:  %hh:~1%%time:~2,1%%mm:~1%%time:~2,1%%ss:~1%%time:~8,1%%cc:~1%

EDIT 2020/06/05: Pass-over-midnight adjustment added

@echo off
setlocal EnableDelayedExpansion

set "startTime=%time: =0%"

set /P "=Any process here..."

set "endTime=%time: =0%"



rem Get elapsed time:
set "end=!endTime:%time:~8,1%=%%100)*100+1!"  &  set "start=!startTime:%time:~8,1%=%%100)*100+1!"
set /A "elap=((((10!end:%time:~2,1%=%%100)*60+1!%%100)-((((10!start:%time:~2,1%=%%100)*60+1!%%100), elap-=(elap>>31)*24*60*60*100"

rem Convert elapsed time to HH:MM:SS:CC format:
set /A "cc=elap%%100+100,elap/=100,ss=elap%%60+100,elap/=60,mm=elap%%60+100,hh=elap/60+100"

echo Start:    %startTime%
echo End:      %endTime%
echo Elapsed:  %hh:~1%%time:~2,1%%mm:~1%%time:~2,1%%ss:~1%%time:~8,1%%cc:~1%

      HH        :      MM        :      SS        .       CC

(((1  HH  %%100)*60+1  MM  %%100)*60+1  SS  %%100)*100+1  CC  %%100

That is, insert (((1 at beginning, replace the colons by %%100)*60+1, replace the point by %%100)*100+1 and insert %%100 at end; finally, evaluate the resulting string as an arithmetic expression. In the time variable there are two different substrings that needs to be replaced, so the conversion must be completed in two lines. To get an elapsed time, use (endTime)-(startTime) expression and replace both time strings in the same line.

@echo off
setlocal EnableDelayedExpansion

set "startTime=%time: =0%"

set /P "=Any process here..."

set "endTime=%time: =0%"



rem Get elapsed time:
set "end=!endTime:%time:~8,1%=%%100)*100+1!"  &  set "start=!startTime:%time:~8,1%=%%100)*100+1!"
set /A "elap=((((1!end:%time:~2,1%=%%100)*60+1!%%100)-((((1!start:%time:~2,1%=%%100)*60+1!%%100)"

rem Convert elapsed time to HH:MM:SS:CC format:
set /A "cc=elap%%100+100,elap/=100,ss=elap%%60+100,elap/=60,mm=elap%%60+100,hh=elap/60+100"

echo Start:    %startTime%
echo End:      %endTime%
echo Elapsed:  %hh:~1%%time:~2,1%%mm:~1%%time:~2,1%%ss:~1%%time:~8,1%%cc:~1%

       HH        :      MM        :      SS        .       CC

(((10  HH  %%100)*60+1  MM  %%100)*60+1  SS  %%100)*100+1  CC  %%100

That is, insert (((10 at beginning, replace the colons by %%100)*60+1, replace the point by %%100)*100+1 and insert %%100 at end; finally, evaluate the resulting string as an arithmetic expression. In the time variable there are two different substrings that needs to be replaced, so the conversion must be completed in two lines. To get an elapsed time, use (endTime)-(startTime) expression and replace both time strings in the same line.

@echo off
setlocal EnableDelayedExpansion

set "startTime=%time: =0%"

set /P "=Any process here..."

set "endTime=%time: =0%"



rem Get elapsed time:
set "end=!endTime:%time:~8,1%=%%100)*100+1!"  &  set "start=!startTime:%time:~8,1%=%%100)*100+1!"
set /A "elap=((((10!end:%time:~2,1%=%%100)*60+1!%%100)-((((10!start:%time:~2,1%=%%100)*60+1!%%100)"

rem Convert elapsed time to HH:MM:SS:CC format:
set /A "cc=elap%%100+100,elap/=100,ss=elap%%60+100,elap/=60,mm=elap%%60+100,hh=elap/60+100"

echo Start:    %startTime%
echo End:      %endTime%
echo Elapsed:  %hh:~1%%time:~2,1%%mm:~1%%time:~2,1%%ss:~1%%time:~8,1%%cc:~1%

       HH        :      MM        :      SS        .       CC

(((10  HH  %%100)*60+1  MM  %%100)*60+1  SS  %%100)*100+1  CC  %%100

That is, insert (((10 at beginning, replace the colons by %%100)*60+1, replace the point by %%100)*100+1 and insert %%100 at end; finally, evaluate the resulting string as an arithmetic expression. In the time variable there are two different substrings that needs to be replaced, so the conversion must be completed in two lines. To get an elapsed time, use (endTime)-(startTime) expression and replace both time strings in the same line.

@echo off
setlocal EnableDelayedExpansion

set "startTime=%time%"

set /P "=Any process here..."

set "endTime=%time%"



rem Get elapsed time:
set "end=!endTime:.=%%100)*100+1!"  &  set "start=!startTime:.=%%100)*100+1!"
set /A "elap=((((10!end::=%%100)*60+1!%%100)-((((10!start::=%%100)*60+1!%%100)"

rem Convert elapsed time to HH:MM:SS:CC format:
set /A "cc=elap%%100+100,elap/=100,ss=elap%%60+100,elap/=60,mm=elap%%60+100,hh=elap/60+100"

echo Start:    %startTime%
echo End:      %endTime%
echo Elapsed:  %hh:~1%:%mm:~1%:%ss:~1%.%cc:~1%

      HH        :      MM        :      SS        .       CC

(((1  HH  %%100)*60+1  MM  %%100)*60+1  SS  %%100)*100+1  CC  %%100

That is, insert (((1 at beginning, replace the colons by %%100)*60+1, replace the point by %%100)*100+1 and insert %%100 at end; finally, evaluate the resulting string as an arithmetic expression. In the time variable there are two different substrings that needs to be replaced, so the conversion must be completed in two lines. To get an elapsed time, use (endTime)-(startTime) expression and replace both time strings in the same line.

EDIT 2017/06/14: Locale independent adjustment added

@echo off
setlocal EnableDelayedExpansion

set "startTime=%time: =0%"

set /P "=Any process here..."

set "endTime=%time: =0%"



rem Get elapsed time:
set "end=!endTime:%time:~8,1%=%%100)*100+1!"  &  set "start=!startTime:%time:~8,1%=%%100)*100+1!"
set /A "elap=((((1!end:%time:~2,1%=%%100)*60+1!%%100)-((((1!start:%time:~2,1%=%%100)*60+1!%%100)"

rem Convert elapsed time to HH:MM:SS:CC format:
set /A "cc=elap%%100+100,elap/=100,ss=elap%%60+100,elap/=60,mm=elap%%60+100,hh=elap/60+100"

echo Start:    %startTime%
echo End:      %endTime%
echo Elapsed:  %hh:~1%%time:~2,1%%mm:~1%%time:~2,1%%ss:~1%%time:~8,1%%cc:~1%