How to get my java to work after deleting the java files from the program file i

i clicked on start menu, entered computers, then into drive C. the i clicked on Program file(x86) and deleted the 'java' folder. i did forgeting that i have to uninstall it first in control panel. i have installed java runtime environment(JRE) 6 update 16 in my computer system, yet, certain softwares which need java to operate cannot do so as these softwares indicates that the JRE is not found in my system. what do i do . i'm in dire need for solutions