If I've understood your question you can access the timer indirectly via alarm() and signal().

Here is a very simple Hello World program for the Raspberry Pi, using wiringPi, that toggles pin 40 and pin 38. Pin 40 is toggled in the main loop and pin 38 from the alarm interrupt signal.

Compile with: gcc -Wall -o helloworld helloworld.c -lwiringPi

Control+c to quit.

I hope this helps,

JSU

helloworld.c

#include <wiringPi.h>
#include <stdlib.h>

#include <signal.h>
#include <unistd.h>

void alarmWakeup(int sig_num);


int main(int argc, char *argv[])
{
    unsigned int j;

    wiringPiSetupPhys();//use the physical pin numbers on the P1 connector


    pinMode(40, OUTPUT);
    pinMode(38, OUTPUT);

    signal(SIGALRM, alarmWakeup);   
    ualarm(5000, 5000);


    while(1)
    {
        digitalWrite(40, HIGH); //pin 40 high
        for(j=0; j<1000000; j++);//do something
        digitalWrite(40, LOW);  //pin 40 low
        for(j=0; j<1000000; j++);//do something
    }

    return 0;

}//int main(int argc, char *argv[])


void alarmWakeup(int sig_num)
{
    unsigned int i;

    if(sig_num == SIGALRM)
    {
        digitalWrite(38, HIGH); //pin 38 high
        for(i=0; i<65535; i++); //do something
        digitalWrite(38, LOW);  //pin 38 low
    }

}

The wiringPi library provides a number of blocking timer calls. One is used for micro second granularity (delayMicroseconds) and the other is used for milli second granularity (delay). See:

http://wiringpi.com/reference/timing/

Using either of these, you can block your C program for a configurable amount of time. For example, if you need to send a pulse every 50 milli seconds, you could code:

while(1)
{
   // Code to send a pulse
   delay(50);
}