Minecraft – can’t use /fill in a command block

Try: /execute <selector> ~ ~ ~ fill <relative coordinates> air 0 replace wool

[EDIT]

If you are wanting the block to disappear after a certain amount of time, say, 30 redstone ticks (60 game ticks), you could summon a WitherSkull below the player and use the execute command on it.

To make the block disappear, you would add a new scoreboard command, lifetime, for instance, and run /scoreboard players add @e[type=WitherSkull] lifetime 1 with a setblock or fill clock, then execute another fill command on every wither skull with a certain lifetime value, like:

/execute @e[type=WitherSkull,score_lifetime_min=31] ~ ~ ~ /fill ~ ~ ~ ~ ~ ~ wool 0 replace air.

Then, you would kill the wither skull: /kill @e[type=WitherSkull,score_lifetime_min=35].

Here is a screenshot of what I did:

if you know the location of the block relative to the command block, you can simply do /execute ~ ~ ~ /[command] and execute the particle effect spawning command at a space relative to the command block, so if you bury it 5 blocks deep and want to make the stone above it smoke, i think you'd do ~0 ~0 ~5 for the location, you'll have to experiment with this on your own, for further details, please look on youtube for "Sethbling" and look at his previous snapshot videos, in which he covered the particle effect feature of the command block.